diff --git a/README.md b/README.md index c311c04..c6ad9e6 100644 --- a/README.md +++ b/README.md @@ -36,85 +36,107 @@ usage: stix -V Verbose mode(print debug information, will increase output file size greatly) ``` +## Example(long-read) -## STIX suite -This repository contains all related tools for using STIX. It includes: - -1. STIX (main program) -2. Giggle (tool for indexing) -3. excord (SV singals extraction for short-read) -4. excordlr (SV singals extraction for long-read) - -The bundled toolset will be published as docker images with version numbers. Please note that the version is NOT the stix version, it is the stix-suite version. - - -### How to use - -Download the docker image with specific version +### Setup demo ``` -docker pull zhengxc1993/stix-suite: - +git clone https://github.com/zhengxinchang/stix.git +cd stix/demo ``` -Run tools - -``` -docker run --rm zhengxc1993/stix-suite: stix +### Build index ``` +# giggle index, takes ~15s +docker run --rm -u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v $(pwd):/wkspace/ zhengxc1993/stix-suite:1.0.1 \ + sh -c "cd /wkspace/; giggle index -i "data/*.bed.gz" -o ./giggle_idx -s -f" +# stix index, takes ~1s +docker run --rm -u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v $(pwd):/wkspace/ zhengxc1993/stix-suite:1.0.1 \ + sh -c "cd /wkspace/; stix -i giggle_idx/ -d stix_idx.db -p meta.ped -c 5" -### Versions +``` -#### 1.0.1 +### Annotate a single SV -- stix[b3fedd9] -- giggle[4071cb7] +**deletion** +``` +# runtime: ~1s +docker run --rm -u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v $(pwd):/wkspace/ zhengxc1993/stix-suite:1.0.1 \ + sh -c "cd /wkspace/; stix \ + -i giggle_idx/ \ + -d stix_idx.db \ + -s 100 \ + -t DEL \ + -l 1:1076253-1076253 \ + -r 1:1076434-1076434 " +``` +output: -- excord[v0.2.4] +``` +stix_run_giggle_query: left:1 1076253 1076253 right:1 1076434 1076434 +Total 0:1 0:1 0:0:0 0:0:0:0 +Giggle_File_Id Sample Sex population Super_population Alt_File Pairend Split +0 demo_hg002_hifi NA NA NA demo_hg002_hifi.bed.gz 0 15 +``` -- excord-lr[v0.1.17] +**insertion** -- stix-merge[1.0.0] +``` +# runtime: ~1s +docker run --rm -u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v $(pwd):/wkspace/ zhengxc1993/stix-suite:1.0.1 \ + sh -c "cd /wkspace/; stix \ + -i giggle_idx/ \ + -d stix_idx.db \ + -s 100 \ + -t INS \ + -l 1:3477303-3477303 \ + -r 1:3477303-3479646 " +``` -
+output -```bash -cd stix-suite -docker build -t stix-suite:1.0.0 -f Dockerfile versions/1.0.1/ -docker tag 784ea063777c zhengxc1993/stix-suite:1.0.1 -docker push zhengxc1993/stix-suite:1.0.1 ``` -
+stix_run_giggle_query: left:1 3477303 3477303 right:1 3477303 3479646 +Total 0:1 0:1 0:0:0 0:0:0:0 +Giggle_File_Id Sample Sex population Super_population Alt_File Pairend Split +0 demo_hg002_hifi NA NA NA demo_hg002_hifi.bed.gz 0 17 +``` -#### 1.0.0 -- stix[b3fedd9] -- giggle[4071cb7] +**Annotate an VCF file** -- excord[v0.2.4] +``` +# runtime: ~2s +docker run --rm -v $(pwd):/wkspace/ zhengxc1993/stix-suite:1.0.1 \ + sh -c "cd /wkspace/; stix \ + -i giggle_idx/ \ + -d stix_idx.db \ + -s 100 \ + -T 5 \ + -f demo-query.vcf \ + | tee ann.vcf 1>/dev/null" -- excord-lr[v0.1.17] +``` -
+output -```bash -stix-suite -docker build -t stix-suite:1.0.0 -f Dockerfile versions/1.0.0/ -docker tag 784ea063777c zhengxc1993/stix-suite:1.0.0 -docker push zhengxc1993/stix-suite:1.0.0 ``` -
+ann.vcf # it should be exactly same with output.ann.vcf. +``` + +For a specific SV,the `STIX_ZERO` and `STIX_ON`E indicate the `number of positive sample` and `number of negative samples` respectively. +The frequency can be calculated with `STIX_ONE/(STIX_ONE + STIX_ZERO)`. -## Example +## Example(short-read) The following example is based on four sample BAMs from the 1000 Genomes project: @@ -222,7 +244,89 @@ stix -i four_alt_db -d four.ped.db -s 500 -f 1kg.four.13.14.vcf.gz ``` -## Build +## Installation/Build + +STIX can be built and run on the Linux system. The installation time on a normal PC usually takes 10-15 minutes, depending on the hardware. + +### STIX suite + +We recommend using the STIX suite image to use STIX and related tools. These tools include: + +1. STIX (main program) +2. Giggle (tool for indexing) +3. excord (SV singals extraction for short-read) +4. excordlr (SV singals extraction for long-read) + +The bundled toolset will be published as docker images with version numbers. Please note that the version is NOT the stix version, it is the stix-suite version. + + +#### How to use + +Download the docker image with specific version + +``` +docker pull zhengxc1993/stix-suite: + +``` + +Run tools + +``` +docker run --rm -u $(id -u):$(id -g) -v /etc/passwd:/etc/passwd zhengxc1993/stix-suite: stix + +``` + + +#### Versions + + +##### 1.0.1 +
+- stix[b3fedd9] + +- giggle[4071cb7] + +- excord[v0.2.4] + +- excord-lr[v0.1.17] + +- stix-merge[1.0.0] + + + +```bash +cd stix-suite +docker build -t stix-suite:1.0.0 -f Dockerfile versions/1.0.1/ +docker tag 784ea063777c zhengxc1993/stix-suite:1.0.1 +docker push zhengxc1993/stix-suite:1.0.1 +``` +
+ + +##### 1.0.0 + +
+ +- stix[b3fedd9] + +- giggle[4071cb7] + +- excord[v0.2.4] + +- excord-lr[v0.1.17] + + +```bash +stix-suite +docker build -t stix-suite:1.0.0 -f Dockerfile versions/1.0.0/ +docker tag 784ea063777c zhengxc1993/stix-suite:1.0.0 +docker push zhengxc1993/stix-suite:1.0.0 +``` +
+ + +### build from source + ``` git clone https://github.com/ryanlayer/giggle.git cd giggle diff --git a/demo/data/demo_hg002_hifi.bed.gz b/demo/data/demo_hg002_hifi.bed.gz new file mode 100644 index 0000000..78e0ca7 Binary files /dev/null and b/demo/data/demo_hg002_hifi.bed.gz differ diff --git a/demo/demo-query.vcf b/demo/demo-query.vcf new file mode 100644 index 0000000..522b338 --- /dev/null +++ b/demo/demo-query.vcf @@ -0,0 +1,88 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##FORMAT= +##FORMAT= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##bcftools_normVersion=1.14+htslib-1.18 +##bcftools_normCommand=norm -m-any -Ou results/draft_benchmarksets/GRCh38_HG002-T2TQ100v1.0-dipz2k_stvar-excluded/intermediates/GRCh38_HG2-T2TQ100-V1.0_stvar_dipcall-z2k.vcf.gz; Date=Thu Nov 9 06:14:30 2023 +##bcftools_normCommand=norm -d exact -Ou; Date=Thu Nov 9 06:14:30 2023 +##bcftools_normCommand=norm -cs -f resources/references/GRCh38.fa -Ov; Date=Thu Nov 9 06:14:30 2023 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_normCommand=norm -m-any -Oz -o results/draft_benchmarksets/GRCh38_HG002-T2TQ100v1.0-dipz2k_stvar-excluded/intermediates/GRCh38_HG2-T2TQ100-V1.0_stvar_dipcall-z2k.trfanno.split_multi.vcf.gz results/draft_benchmarksets/GRCh38_HG002-T2TQ100v1.0-dipz2k_stvar-excluded/intermediates/GRCh38_HG2-T2TQ100-V1.0_stvar_dipcall-z2k.trfanno.vcf.gz; Date=Thu Nov 9 08:35:50 2023 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_filterVersion=1.13+htslib-1.13+ds +##bcftools_filterCommand=filter -i 'abs(SVLEN) > 50 ' HG002_SVs_Tier1_v0.6.benchmark_interbed_alllen.vcf; Date=Fri Jul 26 10:59:51 2024 +##bcftools_viewVersion=1.13+htslib-1.13+ds +##bcftools_viewCommand=view -i 'GT="0|1" || GT="1|1" || GT="10"' ./HG002_SVs_Tier1_v0.6.benchmark_interbed.vcf; Date=Sat Jul 27 20:16:50 2024 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002 +1 1288300 . TCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCCCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCC T 30 PASS TRF;TRFdiff=-4.1;TRFrepeat=CCCGTGTCTCTGCTCCGT;TRFovl=1;TRFstart=1288181;TRFend=1290252;TRFperiod=18;TRFcopies=107.7;TRFscore=4877;TRFentropy=1.55;SVTYPE=DEL;SVLEN=74;LCR=0.748694 GT:AD 0|1:1,1 +1 1288543 . TCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCCCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGTTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGTTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCCCGTGTCCCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCCCCGTCCCGTGTCCCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGCTCCGTCCCGTGTCCCTGCCCCGTCCCGTGTCTCTGCC T 30 PASS TRF;TRFdiff=-42.8;TRFrepeat=CCCGTGTCTCTGCTCCGT;TRFovl=1;TRFstart=1288181;TRFend=1290252;TRFperiod=18;TRFcopies=69;TRFscore=4877;TRFentropy=1.55;SVTYPE=DEL;SVLEN=770;LCR=0.774556 GT:AD 0|1:1,1 +1 1289592 . CTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCCCCGTCCCGTG C 30 PASS TRF;TRFdiff=-14.2;TRFrepeat=CCCGTGTCTCTGCTCCGT;TRFovl=1;TRFstart=1288181;TRFend=1290252;TRFperiod=18;TRFcopies=97.6;TRFscore=4877;TRFentropy=1.55;SVTYPE=DEL;SVLEN=255;LCR=0.767309 GT:AD 0|1:1,1 +1 1349974 . TGGGAGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCTGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGAC T 30 PASS SVTYPE=DEL;SVLEN=1080;LCR=0.752907 GT:AD 1|1:0,2 +1 1605734 . GGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGCGGTGGGCTGGGCTGGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGGGGTCGGATGGTCAGGCGTGGGCTGGGCTGGTCAGGCGTGGGGCGGGCTGGTCAGGCGTGGGCTGGGCTGGGCTGGTCTGGTGTGGACTGGGCTGGTCAGGCGTGGGGTGGGCTGGTCAGGCGTGGGGTCGGCTGGTCAGGTGAGGGGTCGGCTGGTCAGGCGTGGGCTGGGCTGCTCAGGCGTGGGCTGGACTGGTCAGGCGTGGGCTGGGCTGGTCAGGCGTGGGCTGGGCTGGTCAGATGTGGGCTGGGCTGGTCAGGTGAGGGGTC G 30 PASS TRF;TRFdiff=-17.2;TRFrepeat=GGGCTGGGCTGGTCAGGTGT;TRFovl=1;TRFstart=1605379;TRFend=1606635;TRFperiod=20;TRFcopies=44;TRFscore=2443;TRFentropy=1.63;SVTYPE=DEL;SVLEN=345;LCR=0.822883 GT:AD 1|1:0,2 +1 1666974 . ACACGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCAAACCAGAGAAATCCAGCTCTGGGTGACAGAGCAAGACTCTGTTTCGGGAAAAATAAAATACATAGGCAGGGCGCGGTGGCT A 30 PASS SVTYPE=DEL;SVLEN=167;RM_score=124;RM_repeat=ALUSG;RM_clsfam=SINE/Alu;LCR=0.979707 GT:AD 1|1:0,2 +1 2522791 . C CTATAGTGACTTAACGGAGGGCACTGTGTGTGCTATAGTGACTTAACGGAGGGCACCGTGTGTGTTATAGTGACTTAACGGAGGGCACCGTATGGTGCTATAGTGACTTAACGGAGGGCACTGTGTGTGTTATAGTGACTTAACGGAGGGCACCGTGTGTGTTATAGTGACTTAACGGAGGGCACCGTATGGTGCTATAGTGACTTAACGGAGGGCACCGTATGGTGCTATAGTGACTTAACGGAGGGGACCGTGTGGTGCTATAGTGACTTAACGGAGGGCATTGTGTGTGCTATAGTGACTTAACGGAGGGCACCGTACGGTGCTATAGTGACTTAACGGAGGGCACTGTGTGTGCTAAAGTGACTTAACGGAGGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACCGGATGGTGCTATAGTGACTTAACGGAAGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACTGGATGGTGCTATAGTGACTTAACGGAGGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACCGTGTGGTGT 30 PASS TRF;TRFdiff=5.7;TRFrepeat=GGTGCTATAGTGACTTAACAGAGGGCACTGGATGGTGCTATAGTGACTTAACGGAGGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACTGTGT;TRFovl=1;TRFstart=2522689;TRFend=2523009;TRFperiod=98;TRFcopies=9;TRFscore=758;TRFentropy=1.95;TRFsim=0.957;SVTYPE=INS;SVLEN=555;LCR=0.970685 GT:AD 0|1:0,1 +1 2602115 . G GTTCTTAGAGTCAGAGGCCACTCAGCAATCTAGAGGCCACGTCAGGGACCAGCCTCCCTCCAGGTAGAAGTCAGGTTCGTC 30 PASS SVTYPE=INS;SVLEN=80;LCR=0.991794 GT:AD 0|1:1,1 +1 2849419 . A AATTGAACTCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGCCTGGGTGGGAGTGTGGAATGAAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGTCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGCCCTGGGCAGGAGTGTGGAATTGAGCCCCGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGTATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGCGAGTGTGGAATTGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGT 30 PASS TRF;TRFdiff=2.5;TRFrepeat=TGGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCGTGTCCTGGGCGGGAGTGTGGAATTGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAA;TRFovl=1;TRFstart=2848785;TRFend=2849743;TRFperiod=349;TRFcopies=5.2;TRFscore=2415;TRFentropy=1.87;TRFsim=0.959;SVTYPE=INS;SVLEN=882;LCR=0.929351 GT:AD 0|1:1,1 +1 2849432 . G GCCTGGGCGGGAGTGTGGAATGGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGCCTGGGTGGGAGTGTGGAATGAAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGCCCTGGGCAGGAGTGTGGAATTGAGCCCCGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTTTCCTGGGTGGGAGTGTGGTATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGCGAGTGTGGAATTGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATGGAACCCTGTGC 30 PASS TRF;TRFdiff=2.3;TRFrepeat=TGGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCGTGTCCTGGGCGGGAGTGTGGAATTGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAA;TRFovl=1;TRFstart=2848785;TRFend=2849743;TRFperiod=349;TRFcopies=5;TRFscore=2415;TRFentropy=1.87;TRFsim=0.956;SVTYPE=INS;SVLEN=788;LCR=0.930305 GT:AD 1|0:1,1 +1 2859500 . A AAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAAGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGAAGGAAGGAGGG 30 PASS TRF;TRFdiff=42.9;TRFrepeat=GGAGGAAGGAA;TRFovl=1;TRFstart=2859183;TRFend=2859623;TRFperiod=11;TRFcopies=84.1;TRFscore=668;TRFentropy=1.1;TRFsim=0.933;SVTYPE=INS;SVLEN=472;RM_score=214;RM_repeat=GA-RICH;RM_clsfam=Low_complexity;LCR=0.510721 GT:AD 1|0:1,1 +1 2859528 . G GGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACA 30 PASS TRF;TRFdiff=155.1;TRFrepeat=GGAGGAAGGAA;TRFovl=1;TRFstart=2859183;TRFend=2859623;TRFperiod=11;TRFcopies=196.3;TRFscore=668;TRFentropy=1.1;TRFsim=0.933;SVTYPE=INS;SVLEN=1706;RM_score=739;RM_repeat=GA-RICH;RM_clsfam=Low_complexity;LCR=0.509119 GT:AD 0|1:1,1 +1 2859564 . A AAGGAACAAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGAGGAGGAAGGAAGGAGGGAGGAAG 30 PASS TRF;TRFdiff=19.7;TRFrepeat=GGAGGAAGGAA;TRFovl=1;TRFstart=2859183;TRFend=2859623;TRFperiod=11;TRFcopies=60.9;TRFscore=668;TRFentropy=1.1;TRFsim=0.903;SVTYPE=INS;SVLEN=217;RM_score=78;RM_repeat=G-RICH;RM_clsfam=Low_complexity;LCR=0.541784 GT:AD 1|0:1,1 +1 3016686 . A AGGGACGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGAGAGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGAGAGGAAAGGAAGAAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAGGGAGGGAGGGAGGAAGGGAAGGAGAGAAGGAGAAAGAAGTGAGGAAAGAAGGAGGGAGGGGAGAGAAAATGGAGGAAGGAGGATGGGAACAGGGGAGGGAGAGAAGGAGGAAGGAAGGAGGGAAGGAGATACGTAGGAAGGAAGGAGGGAAAAAGGAAGAGAGAAAGGGAAGGAAGGAGGGAGGAAGGGAGGAAGGAAGGAGAGAGGGAGGGCAGGAGGAGGGGAGGGAGGGAGGAAGGGAAGAAGGGAGGGGAGAGGAAGAGCAGGAGGAAGGTAAGGAGGGAGGAGGGATGGAGAAGGGAGGGAGGGAGGAAGCGAGGAGGAGAGGGAGGGAGGATGGTGGGAGGGAGGGAGGGGGGAAGC 30 PASS TRF;TRFdiff=0;TRFrepeat=GAGG;TRFovl=1;TRFstart=3016323;TRFend=3017292;TRFperiod=4;TRFcopies=250;TRFscore=1126;TRFentropy=1.15;SVTYPE=INS;SVLEN=582;RM_score=281;RM_repeat=G-RICH;RM_clsfam=Low_complexity;LCR=0.567352 GT:AD 0|1:0,1 +1 3016686 . A AGGGACGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGAGAGAGGAAGGGAAGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGAGAGGAAAGGAAGAAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAGGGAGGGAGGGAGGAAGGGAAGGAGAGAAGGAGAAAGAAGTGAGGAAAGAAGGAGGGAGGGGAGAGAAAATGGAGGAAGGAGGATGGGAACAGGGGAGGGAGAGAAGGAGGAAGGAAGGAGGGAAGGAGATACGTAGGAAGGAAGGAGGGAAAAAGGAAGAGAGAAAGGGAAGGAAGGAGGGAGGAAGGGAGGAAGGAAGGAGAGAGGGAGGGCAGGAGGAGGGGAGGGAGGGAGGAAGGGAAGGGAGGGGAGAGGAAGAGCAGGAGGAAGGTAAGGAGGGAGGAGGGATGGAGAAGGGAGGGAGGGAGGAAGCGAGGAGGAGAGGGAGGGAGGATGGTGGGAGGGAGGGAGGGGGGAAGC 30 PASS TRF;TRFdiff=0;TRFrepeat=AGAGAGGAAAGGAAGGAGGGAGGGAGG;TRFovl=1;TRFstart=3016309;TRFend=3017262;TRFperiod=27;TRFcopies=35.9;TRFscore=1150;TRFentropy=1.14;SVTYPE=INS;SVLEN=579;RM_score=280;RM_repeat=G-RICH;RM_clsfam=Low_complexity;LCR=0.567141 GT:AD 1|0:0,1 +4 166755885 . TAAGAGATTTGGGACAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAGCGACGCAGAAGACGGTGATTTCTGCATTTCCATCTGAGGTACCGGGTTCATCTCACTAGGGAGTGCCAGACAGTGGGCGCAGGCCAGTGTGTGTGCGCACCGTGCGCGAGCCGAAGCAGGGCGAGGCATTGCCTCACCTGGGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCGAGTCAAAGAAAGGGGTGACGGTCGCACCTGGAAAATCAGGTCACTCCCACCCGAATATTGCGCTTTTCAGACCGGCTTAAGAAACGGCGCACCACGAGACTATATCCCACACCTGGCTCGGAGGGTCCTACGCCCACGGAATCTCGCTGATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAGGCGGCAACGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGCTTAGGTAAACAAAGCAGCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTGTAGGCTCCACCTCTGGGGGCAGGGCACAGACAAACAAAAAGACAGCAGTAACCTCTGCAGACTTAAGTGTCCCTGTCTGACAGCTTTGAAGAGAGCAGTAGTTCTCCCAGCACGCAGATGGAGATCTGAGAACGGGCAGACAGACTGCCTCCTCAAGTGGGTCCCTGACTCCTGACCCCCGAGCAGCCTAACTGGGAGGCACCCCCCAGCAGGGGCACACTGACACCTCACACGGCAGGGTATTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTTAGAAGGAAAACTAACAACCAGAAAGGACATCTACACCGAAAACCCATCTGTACATCACCATCATCAAAGACCAAAAGTAGATAAAACCACAAAGATGGGGAAAAAACAGAACAGAAAAACTGGAAACTCTAAAACGCAGAGCGCCTCTCCTCCTCCAAAGGAATGCAGTTCCTCACCAGCAACAGAACAAAGCTGGATGGAGAATGATTTTGACGAGCTGAGAGAAGAAGGCTTCAGACGATCAAATTACTCTGAGCTACGGGAGGACATTCAAACCAAAGGCAAAGAAGTTGAAAACTTTGAAAAAAATTTAGAAGAATGTATAACTAGAATAACCAATACAGAGAAGTGCTTAAAGGAGCTGATGGAGCTGAAAACCAAGGCTCGAGAACTACGTGAAGAATGCAGAAGCCTCAGGAGCCGATGCGATCAACTGGAAGAAAGGGTATCAGCAATGGAAGATGAAATGAATGAAATGAAGCGAGAAGGGAAGTTTAGAGAAAAAAGAATAAAAAGAAATGAGCAAAGCCTCCAAGAAATATGGGACTATGTGAAAAGACCAAATCTACGTCTGATTGGTGTACCTGAAAGTGATGTGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTATCCAGGAGAACTTCCCCAATCTAGCAAGGCAGGCCAACGTTCAGATTCAGGAAATACAGAGAACGCCACAAAGATACTCCTCGAGAAGAGCAACTCCAAGACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGTTAAGGGCAGCCAGAGAGAAAGGTCGGGTTACCCTCAAAGGAAAGCCCATCAGACTAACAGCGGATCTCTCGGCAGAAACCCTACAAGCCAGAAGAGAGTGGGGGCCAATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTATAGACAAGCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCCCTAAAAGAGCTCCTGAAGGAAGCGCTAAACATGGAAAGGAACAACCGGTACCAGCCGCTGCAAAATCATGCCAAAATGTAAAGACCATCGAGACTAGGAAGAAACTGCATCAACTAATGAGCAAAATCACCAGCTAACATCATAATGACAGGATCAAATTCACACATAACAATATTAACTTTAAATATAAATGGACTAAATTCTGCAATTAAAAGACACAGACTGGCAAGTTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACGTGCAGAGACACACATAGGCTCAAAATAAAAGGATGGAGGAAGATCTACCAAGCCAATGGAAAACAAAAAAAGGCAGGGGTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATCAAAAGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATTCAACAAGAGGAGCTAACTATCCTAAATATTTATGCACCCAATACAGGAGCACCCAGATTCATAAAGCAAGTCCTCAGTGACCTACAAAGAGACTTAGACTCCCACACATTAATAATGGGAGACTTTAACACCCCACTGTCAACATTAGACAGATCAACGAGACAGAAAGTCAACAAGGATACCCAGGAATTGAACTCAGCTCTGCACCAAGCAGACCTAATAGACATCTACAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTCAGCACCACACCACACCTATTCCAAAATTGACCACATAGTTGGAAGTAAAGCTCTCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTATCTCTCAGACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAATCTCACTCAAAGCCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACGAAATGAACGCAGAAATAAAGATGTTCTTTGAAACCAACAAGAACAAAGACACCACATACCAGAATCTCTGGGACGCATTCAAAGCAGTGTGTAGAGGGAAATTTATAGCACTAAATGCCTACAAGAGAAAGCAGGAAAGATCCAAAATTGACACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACACATTCAAAAGCTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGGAAATAGAGACACAAAAAACCCTTCAAAAAATCAATGAATCCAGGAGCTGGTTTTTTGAAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAAAAAAGAGAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGGATATCACCACCGATCCCACAGAAATACAAACTACCATCAGAGAATACTACAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATACATTCCTCGACACATACACTCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGTGGCAATAATCAATAGTTTACCAACCAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGTACATGGAGGAACTGGTACCATTCCTTCTGAAACTATTCCAATCAATAGAAAAAGAGGGAATCCTCCCTAACTCATTTTATGAGGCCAGCATCATTCTGATACCAAAGCCGGGCAGAGACACAACCAAAAAAGAGAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCAAATCAATAAATGTAATCCAGCATATAAACAGAGCCAAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAAGCCTTTGACAAAATTCAACAACCCTTCATGCTAAAAACTCTCAATAAATTAGGTATTGATGGGACGTATTTCAAAATAATAAGAGCTATCTATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACCGGCACAAGACAGGGATGCCCTCTCTCACCGCTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGGCAGGAGAAGGAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTTGCAGACGACATGATTGTATATCTAGAAAACCCCATCGTCTCAGCCCAAAATCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAATCACAAGCATTCTTATACACCAACAACAGACAAACAGAGAGCCAAATCATGGGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAAGGAAATAAAAGAGGAGACAAACAAATGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACATCATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACATCCCATTACTGGGTATATACCCAAATGAGTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGACCCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAA T 30 PASS SVTYPE=DEL;SVLEN=6035;RM_score=4103;RM_repeat=L1HS;RM_clsfam=LINE/L1;LCR=0.96705 GT:AD 1|1:0,2 +4 167451236 . GGATATATATCCATATATTCACATATATGGATATATATCCATATATTCACATATAT G 30 PASS TRF;TRFdiff=-2;TRFrepeat=ATATATATATCCATATATTCACATATATG;TRFovl=1;TRFstart=167450892;TRFend=167451737;TRFperiod=28;TRFcopies=28;TRFscore=2031;TRFentropy=1.59;SVTYPE=DEL;SVLEN=55;LCR=0.866044 GT:AD 0|1:1,1 +4 167451519 . TATATATCATATATTCACATATATGATATATATATCATATATTCACATATATGATATATATATCATATATTCACATATATG T 30 PASS TRF;TRFdiff=-2.9;TRFrepeat=ATATATATATCCATATATTCACATATATG;TRFovl=1;TRFstart=167450892;TRFend=167451737;TRFperiod=28;TRFcopies=27.1;TRFscore=2031;TRFentropy=1.59;SVTYPE=DEL;SVLEN=80;RM_score=36;RM_repeat=(TA)N;RM_clsfam=Simple_repeat;LCR=0.788549 GT:AD 0|1:1,1 +4 167787682 . TATTTAATTATTTAACAAATAAATTATTTAATTATTTAACAAATAAATTATTTAATTATTTAACAAATAAATAAATTATTTAATTATTTAACAAATAAATAAATCATTTAATTATTTAACAAATAAATC T 30 PASS TRF;TRFdiff=-5.3;TRFrepeat=ATTTAAATTTAAATTTATTTATGTAAGCA;TRFovl=1;TRFstart=167787487;TRFend=167788087;TRFperiod=24;TRFcopies=17.3;TRFscore=200;TRFentropy=1.28;SVTYPE=DEL;SVLEN=128;RM_score=50;RM_repeat=(TAAT)N;RM_clsfam=Simple_repeat;LCR=0.622694 GT:AD 0|1:1,1 +4 169178281 . TAAATAAGCAACTATGCTTATTTAAAAAAATAAGCAACTATGCTTATTTAAAA T 30 PASS SVTYPE=DEL;SVLEN=52;LCR=0.833695 GT:AD 1|1:0,2 +4 169357309 . CCTGTAATCCCAGCACTTTGTGAGGCTGAGGTGGGAGGATTGCTTGAGGTCTGGAGTTCGAGACTAGGCTGGGAAGCAAAGCAAGACTCTGTCTCTACAAAAATTTAAAAGTTAGCTGAACATGGTCATGTACACCTGTAGACCCAGCTACCTGAGAGGCTGAGGTGGGAGGACTGCTTGAGTCTAGGAGTTTGAGACTGCAGTGAGTCATGATTTTGCCACTGGACTCCAGCCTGTGTGACAGAGTAAAATCCTGTCTCAAAAAAAAAGAATTATTAATGAGTATGTAGAACATTGATTCCACTTCTTCAGAATGCACATTCTTTTAGGAAAAAGTATATCTCAACAAATTTTAACTAACTGGTATCATATAAAAAAAAAATCAGCAAACTATGCTGTGTAGGCCAAACCCAGCTTGCCAT C 30 PASS SVTYPE=DEL;SVLEN=421;LCR=0.98677 GT:AD 1|1:0,2 +10 131377105 . C CCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCTACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCAT 30 PASS TRF;TRFdiff=8;TRFrepeat=GAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTG;TRFovl=1;TRFstart=131376784;TRFend=131377282;TRFperiod=59;TRFcopies=16.5;TRFscore=1467;TRFentropy=1.81;TRFsim=0.996;SVTYPE=INS;SVLEN=472;LCR=0.906094 GT:AD 0|1:0,1 +10 131486818 . T TATGTGTGTTTATGCCCATGTTCACATGTGTACACTATGTGTATGTGTGTTTATGCTCATGTTTGCATGTATACATTATGTGTATGTGTGTTTATGCTCATGTTTGCATGTGTACATGTGTATGTGTGTTTATGCCCATGTTCACATGTGTACATTATGTGTATGTGTGTTTATGCCCATGTTCACATGTGTACATTATGTGTATGTGTGTTTATGCTCATGTTTGCATGTGTACATGTGTATGTGTGTTTATGCTCATGTTCACGTGTGTACATTATGTGTATGTGTTTATGCTCATGTTCGCATGTGTACATTATGTGTATGTGTGTTTATGCTCATGTTCACATGTGTACATTATGTGTATGTGTGTTTATGCCCATGTTCACACGTGTACATTATGTGTATGTGTGTTTATGCTC 30 PASS TRF;TRFdiff=10.2;TRFrepeat=TGTATGTGTGTTTATGCTCATGTTCACATGTGTACATTATG;TRFovl=1;TRFstart=131486495;TRFend=131487110;TRFperiod=41;TRFcopies=25.3;TRFscore=979;TRFentropy=1.81;TRFsim=0.925;SVTYPE=INS;SVLEN=418;LCR=0.918294 GT:AD 1|1:0,2 +10 131512437 . G GTATATGTTATGTGTGTGTGGCCCCTGTGCCTTGTGCTTATGCATATGTACTGTGTGTTGTGAGTATATGTTGTGTGTGTAATGTGCATGTTGTGCATGGTGTGTATGTTGTGTACGTATGTTTATGTGTATATGCATGTGTCTTGTGTTTTGGGTGTATGTTGTGTGTATGTGTGGAGTGTATGATTTATGTGTGTGCACATATATTATGTGTTGTGGGTGCATTTTGTGTGAGTGTACATGTTGTATTGTATGTTCTATGTGTGGTGTGTAGGGCTATGTGTGTATGTTTGTGTCATGTGCGTTTTGGGTGTATGTTGTGTACATGTGTGGTGTGCATGGTTTATGTGTGTGCATATGTTATGTGTTGTGGGTGTGTGTTGTGTGTGTGCATGTGTTTTGTGTTCTTTGTGTGGTGTGTCTGTTTATGTGTGTATGTGTGTGTCATGTGTGTTTTGGGTGTGTGTTATGTATATGTGTGGTGTGTATGGTTTA 30 PASS TRF;TRFdiff=0;TRFrepeat=ATGTGTTGTGGGTGTGTGTTGTGTGTGTGCATGTGTTTATGTGTTCTTTGTGTGGTGTGTATGTTTATGTGTGTATGTGTGTGTCATGTGTGTTTTGGGTGTATGTTATGTGTATGTGTGGTGTGTATGGTTTATGTGTGTGCATATGTTGTGTGTTGTGGGTGTGTGTTGTGTGTGCATGTGTTGTATTGTATGTTCTTGTGTGGTGTGTATGTTTATGTGTGTATGTATGTGTCTTGTGCGCTTTGGGTGTATGTTATGTATATGTGTGGTGTGCATGGTTTATGTGTGTGCATATGTT;TRFovl=1;TRFstart=131512177;TRFend=131513230;TRFperiod=301;TRFcopies=3.4;TRFscore=1729;TRFentropy=1.61;SVTYPE=INS;SVLEN=494;RM_score=127;RM_repeat=(TG)N;RM_clsfam=Simple_repeat;LCR=0.823445 GT:AD 1|1:0,2 +10 131623844 . A AGAGAGGTGGGAGAGAGGTGGGGGAGAGAGGTGGGGGGAGGTGGGGGAGGGAGGTGGGGGAGAGAGGTGGGG 30 PASS TRF;TRFdiff=6.5;TRFrepeat=TGGGGGAGAGG;TRFovl=1;TRFstart=131623175;TRFend=131625010;TRFperiod=11;TRFcopies=166;TRFscore=3745;TRFentropy=1.21;TRFsim=0.922;SVTYPE=INS;SVLEN=71;LCR=0.561304 GT:AD 1|0:0,1 +10 131623844 . A AGAGAGGTGGGGGAGAGAGGTGGGGGGAGGTGGGGGAGGGAGGTGGGGGAGAGAGGTGGGG 30 PASS TRF;TRFdiff=0;TRFrepeat=GAGAGGTGGGG;TRFovl=1;TRFstart=131622966;TRFend=131625070;TRFperiod=11;TRFcopies=181.9;TRFscore=4278;TRFentropy=1.2;SVTYPE=INS;SVLEN=60;LCR=0.548613 GT:AD 0|1:0,1 +10 131624691 . G GGGAGAGAGGTGGGGAAGAGGTGGGGGAGAGGTGGGGGAGAGGTGGGGGAGAGGTGGGGGGAGGTGGGGGAGAGAGAT 30 PASS TRF;TRFdiff=0;TRFrepeat=GAGAGGTGGGG;TRFovl=1;TRFstart=131622966;TRFend=131625087;TRFperiod=11;TRFcopies=183.9;TRFscore=4342;TRFentropy=1.2;SVTYPE=INS;SVLEN=77;LCR=0.579225 GT:AD 1|1:0,2 diff --git a/demo/meta.ped b/demo/meta.ped new file mode 100644 index 0000000..888d4ee --- /dev/null +++ b/demo/meta.ped @@ -0,0 +1,2 @@ +Sample Sex population Super_population Alt_File +demo_hg002_hifi NA NA NA demo_hg002_hifi.bed.gz \ No newline at end of file diff --git a/demo/output.ann.vcf b/demo/output.ann.vcf new file mode 100644 index 0000000..a9dcafd --- /dev/null +++ b/demo/output.ann.vcf @@ -0,0 +1,93 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##FORMAT= +##FORMAT= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##bcftools_normVersion=1.14+htslib-1.18 +##bcftools_normCommand=norm -m-any -Ou results/draft_benchmarksets/GRCh38_HG002-T2TQ100v1.0-dipz2k_stvar-excluded/intermediates/GRCh38_HG2-T2TQ100-V1.0_stvar_dipcall-z2k.vcf.gz; Date=Thu Nov 9 06:14:30 2023 +##bcftools_normCommand=norm -d exact -Ou; Date=Thu Nov 9 06:14:30 2023 +##bcftools_normCommand=norm -cs -f resources/references/GRCh38.fa -Ov; Date=Thu Nov 9 06:14:30 2023 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_normCommand=norm -m-any -Oz -o results/draft_benchmarksets/GRCh38_HG002-T2TQ100v1.0-dipz2k_stvar-excluded/intermediates/GRCh38_HG2-T2TQ100-V1.0_stvar_dipcall-z2k.trfanno.split_multi.vcf.gz results/draft_benchmarksets/GRCh38_HG002-T2TQ100v1.0-dipz2k_stvar-excluded/intermediates/GRCh38_HG2-T2TQ100-V1.0_stvar_dipcall-z2k.trfanno.vcf.gz; Date=Thu Nov 9 08:35:50 2023 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_filterVersion=1.13+htslib-1.13+ds +##bcftools_filterCommand=filter -i 'abs(SVLEN) > 50 ' HG002_SVs_Tier1_v0.6.benchmark_interbed_alllen.vcf; Date=Fri Jul 26 10:59:51 2024 +##bcftools_viewVersion=1.13+htslib-1.13+ds +##bcftools_viewCommand=view -i 'GT="0|1" || GT="1|1" || GT="10"' ./HG002_SVs_Tier1_v0.6.benchmark_interbed.vcf; Date=Sat Jul 27 20:16:50 2024 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002 +1 1288300 . TCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCCCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCC T 30 PASS TRF;TRFdiff=-4.1;TRFrepeat=CCCGTGTCTCTGCTCCGT;TRFovl=1;TRFstart=1288181;TRFend=1290252;TRFperiod=18;TRFcopies=107.7;TRFscore=4877;TRFentropy=1.55;SVTYPE=DEL;SVLEN=74;LCR=0.748694;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +1 1288543 . TCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCCCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGTTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGTTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCCCGTGTCCCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCCCCGTCCCGTGTCCCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGCTCCGTCCCGTGTCCCTGCCCCGTCCCGTGTCTCTGCC T 30 PASS TRF;TRFdiff=-42.8;TRFrepeat=CCCGTGTCTCTGCTCCGT;TRFovl=1;TRFstart=1288181;TRFend=1290252;TRFperiod=18;TRFcopies=69;TRFscore=4877;TRFentropy=1.55;SVTYPE=DEL;SVLEN=770;LCR=0.774556;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +1 1289592 . CTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGAGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCGTGTCCCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCCCTGCTCCGTCCCGTGTCTCTGCTCCGTCCCCCGTGTCTCTGCCCCGTCCCGTG C 30 PASS TRF;TRFdiff=-14.2;TRFrepeat=CCCGTGTCTCTGCTCCGT;TRFovl=1;TRFstart=1288181;TRFend=1290252;TRFperiod=18;TRFcopies=97.6;TRFscore=4877;TRFentropy=1.55;SVTYPE=DEL;SVLEN=255;LCR=0.767309;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +1 1349974 . TGGGAGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCTGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACGGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGACGGGGGGAGTGAGGAGGGGGCCTGGACCGGGCAGGAGCGAC T 30 PASS SVTYPE=DEL;SVLEN=1080;LCR=0.752907;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +1 1605734 . GGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGCGGTGGGCTGGGCTGGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGGGGTCGGATGGTCAGGCGTGGGCTGGGCTGGTCAGGCGTGGGGCGGGCTGGTCAGGCGTGGGCTGGGCTGGGCTGGTCTGGTGTGGACTGGGCTGGTCAGGCGTGGGGTGGGCTGGTCAGGCGTGGGGTCGGCTGGTCAGGTGAGGGGTCGGCTGGTCAGGCGTGGGCTGGGCTGCTCAGGCGTGGGCTGGACTGGTCAGGCGTGGGCTGGGCTGGTCAGGCGTGGGCTGGGCTGGTCAGATGTGGGCTGGGCTGGTCAGGTGAGGGGTC G 30 PASS TRF;TRFdiff=-17.2;TRFrepeat=GGGCTGGGCTGGTCAGGTGT;TRFovl=1;TRFstart=1605379;TRFend=1606635;TRFperiod=20;TRFcopies=44;TRFscore=2443;TRFentropy=1.63;SVTYPE=DEL;SVLEN=345;LCR=0.822883;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +1 1666974 . ACACGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCAAACCAGAGAAATCCAGCTCTGGGTGACAGAGCAAGACTCTGTTTCGGGAAAAATAAAATACATAGGCAGGGCGCGGTGGCT A 30 PASS SVTYPE=DEL;SVLEN=167;RM_score=124;RM_repeat=ALUSG;RM_clsfam=SINE/Alu;LCR=0.979707;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +1 2522791 . C CTATAGTGACTTAACGGAGGGCACTGTGTGTGCTATAGTGACTTAACGGAGGGCACCGTGTGTGTTATAGTGACTTAACGGAGGGCACCGTATGGTGCTATAGTGACTTAACGGAGGGCACTGTGTGTGTTATAGTGACTTAACGGAGGGCACCGTGTGTGTTATAGTGACTTAACGGAGGGCACCGTATGGTGCTATAGTGACTTAACGGAGGGCACCGTATGGTGCTATAGTGACTTAACGGAGGGGACCGTGTGGTGCTATAGTGACTTAACGGAGGGCATTGTGTGTGCTATAGTGACTTAACGGAGGGCACCGTACGGTGCTATAGTGACTTAACGGAGGGCACTGTGTGTGCTAAAGTGACTTAACGGAGGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACCGGATGGTGCTATAGTGACTTAACGGAAGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACTGGATGGTGCTATAGTGACTTAACGGAGGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACCGTGTGGTGT 30 PASS TRF;TRFdiff=5.7;TRFrepeat=GGTGCTATAGTGACTTAACAGAGGGCACTGGATGGTGCTATAGTGACTTAACGGAGGGGACCGTGTGGTGTTATAGTGACTTAACGGAGGGCACTGTGT;TRFovl=1;TRFstart=2522689;TRFend=2523009;TRFperiod=98;TRFcopies=9;TRFscore=758;TRFentropy=1.95;TRFsim=0.957;SVTYPE=INS;SVLEN=555;LCR=0.970685;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:0,1 +1 2602115 . G GTTCTTAGAGTCAGAGGCCACTCAGCAATCTAGAGGCCACGTCAGGGACCAGCCTCCCTCCAGGTAGAAGTCAGGTTCGTC 30 PASS SVTYPE=INS;SVLEN=80;LCR=0.991794;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +1 2849419 . A AATTGAACTCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGCCTGGGTGGGAGTGTGGAATGAAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGTCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGCCCTGGGCAGGAGTGTGGAATTGAGCCCCGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGTATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGCGAGTGTGGAATTGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGT 30 PASS TRF;TRFdiff=2.5;TRFrepeat=TGGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCGTGTCCTGGGCGGGAGTGTGGAATTGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAA;TRFovl=1;TRFstart=2848785;TRFend=2849743;TRFperiod=349;TRFcopies=5.2;TRFscore=2415;TRFentropy=1.87;TRFsim=0.959;SVTYPE=INS;SVLEN=882;LCR=0.929351;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +1 2849432 . G GCCTGGGCGGGAGTGTGGAATGGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGCCTGGGTGGGAGTGTGGAATGAAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGCCCTGGGCAGGAGTGTGGAATTGAGCCCCGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAGCCCTGTTTCCTGGGTGGGAGTGTGGTATTGAACCCTGTGCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGCGAGTGTGGAATTGAACCCTGTGCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATGGAACCCTGTGC 30 PASS TRF;TRFdiff=2.3;TRFrepeat=TGGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGAGCCCTGTGCCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAATTGAGCCCTGTGTCCTGGGTGGGAGTGTGGAATGGAACCCTGTGCCCTGGGTGGGAGTGTGGAATTGAGCCCGTGTCCTGGGCGGGAGTGTGGAATTGAACCCTGTGTCCTGGGCGGGAGTGTGGAATGGAACCCTGTGCCCTGGGCGGGAGTGTGGAA;TRFovl=1;TRFstart=2848785;TRFend=2849743;TRFperiod=349;TRFcopies=5;TRFscore=2415;TRFentropy=1.87;TRFsim=0.956;SVTYPE=INS;SVLEN=788;LCR=0.930305;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|0:1,1 +1 2859500 . A AAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAAGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGAAGGAAGGAGGG 30 PASS TRF;TRFdiff=42.9;TRFrepeat=GGAGGAAGGAA;TRFovl=1;TRFstart=2859183;TRFend=2859623;TRFperiod=11;TRFcopies=84.1;TRFscore=668;TRFentropy=1.1;TRFsim=0.933;SVTYPE=INS;SVLEN=472;RM_score=214;RM_repeat=GA-RICH;RM_clsfam=Low_complexity;LCR=0.510721;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|0:1,1 +1 2859528 . G GGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACAAGGGGGGGAGGAGGGAGGAAGAGGAAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGAGGGAGGAACA 30 PASS TRF;TRFdiff=155.1;TRFrepeat=GGAGGAAGGAA;TRFovl=1;TRFstart=2859183;TRFend=2859623;TRFperiod=11;TRFcopies=196.3;TRFscore=668;TRFentropy=1.1;TRFsim=0.933;SVTYPE=INS;SVLEN=1706;RM_score=739;RM_repeat=GA-RICH;RM_clsfam=Low_complexity;LCR=0.509119;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +1 2859564 . A AAGGAACAAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGGAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAGGAAGGAGGGAAGAAGAGGAAGGAACAAGGGGGGGAGGAGGAAGGAAGGAGGGAGGAAGAGGAAGGAGGGAGGAAGAGGAAGGAACAAGGGGGGAGGAGGAAGGAAGGAGGGAGGAAG 30 PASS TRF;TRFdiff=19.7;TRFrepeat=GGAGGAAGGAA;TRFovl=1;TRFstart=2859183;TRFend=2859623;TRFperiod=11;TRFcopies=60.9;TRFscore=668;TRFentropy=1.1;TRFsim=0.903;SVTYPE=INS;SVLEN=217;RM_score=78;RM_repeat=G-RICH;RM_clsfam=Low_complexity;LCR=0.541784;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|0:1,1 +1 3016686 . A AGGGACGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGAGAGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGAGAGGAAAGGAAGAAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAGGGAGGGAGGGAGGAAGGGAAGGAGAGAAGGAGAAAGAAGTGAGGAAAGAAGGAGGGAGGGGAGAGAAAATGGAGGAAGGAGGATGGGAACAGGGGAGGGAGAGAAGGAGGAAGGAAGGAGGGAAGGAGATACGTAGGAAGGAAGGAGGGAAAAAGGAAGAGAGAAAGGGAAGGAAGGAGGGAGGAAGGGAGGAAGGAAGGAGAGAGGGAGGGCAGGAGGAGGGGAGGGAGGGAGGAAGGGAAGAAGGGAGGGGAGAGGAAGAGCAGGAGGAAGGTAAGGAGGGAGGAGGGATGGAGAAGGGAGGGAGGGAGGAAGCGAGGAGGAGAGGGAGGGAGGATGGTGGGAGGGAGGGAGGGGGGAAGC 30 PASS TRF;TRFdiff=0;TRFrepeat=GAGG;TRFovl=1;TRFstart=3016323;TRFend=3017292;TRFperiod=4;TRFcopies=250;TRFscore=1126;TRFentropy=1.15;SVTYPE=INS;SVLEN=582;RM_score=281;RM_repeat=G-RICH;RM_clsfam=Low_complexity;LCR=0.567352;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:0,1 +1 3016686 . A AGGGACGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGAGAGAGGAAGGGAAGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAAGGAGGGAGGGAGGGAGGAGGGAGGGAGGAGAGAGGAAAGGAAGAAGGGAGGGAGGGAGGAGGGAGGGAGGAGGGAGGAAGGGAGGGAGGGAGGGAGGAAGGGAAGGAGAGAAGGAGAAAGAAGTGAGGAAAGAAGGAGGGAGGGGAGAGAAAATGGAGGAAGGAGGATGGGAACAGGGGAGGGAGAGAAGGAGGAAGGAAGGAGGGAAGGAGATACGTAGGAAGGAAGGAGGGAAAAAGGAAGAGAGAAAGGGAAGGAAGGAGGGAGGAAGGGAGGAAGGAAGGAGAGAGGGAGGGCAGGAGGAGGGGAGGGAGGGAGGAAGGGAAGGGAGGGGAGAGGAAGAGCAGGAGGAAGGTAAGGAGGGAGGAGGGATGGAGAAGGGAGGGAGGGAGGAAGCGAGGAGGAGAGGGAGGGAGGATGGTGGGAGGGAGGGAGGGGGGAAGC 30 PASS TRF;TRFdiff=0;TRFrepeat=AGAGAGGAAAGGAAGGAGGGAGGGAGG;TRFovl=1;TRFstart=3016309;TRFend=3017262;TRFperiod=27;TRFcopies=35.9;TRFscore=1150;TRFentropy=1.14;SVTYPE=INS;SVLEN=579;RM_score=280;RM_repeat=G-RICH;RM_clsfam=Low_complexity;LCR=0.567141;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|0:0,1 +4 166755885 . TAAGAGATTTGGGACAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAGCGACGCAGAAGACGGTGATTTCTGCATTTCCATCTGAGGTACCGGGTTCATCTCACTAGGGAGTGCCAGACAGTGGGCGCAGGCCAGTGTGTGTGCGCACCGTGCGCGAGCCGAAGCAGGGCGAGGCATTGCCTCACCTGGGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCGAGTCAAAGAAAGGGGTGACGGTCGCACCTGGAAAATCAGGTCACTCCCACCCGAATATTGCGCTTTTCAGACCGGCTTAAGAAACGGCGCACCACGAGACTATATCCCACACCTGGCTCGGAGGGTCCTACGCCCACGGAATCTCGCTGATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAGGCGGCAACGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGCTTAGGTAAACAAAGCAGCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTGTAGGCTCCACCTCTGGGGGCAGGGCACAGACAAACAAAAAGACAGCAGTAACCTCTGCAGACTTAAGTGTCCCTGTCTGACAGCTTTGAAGAGAGCAGTAGTTCTCCCAGCACGCAGATGGAGATCTGAGAACGGGCAGACAGACTGCCTCCTCAAGTGGGTCCCTGACTCCTGACCCCCGAGCAGCCTAACTGGGAGGCACCCCCCAGCAGGGGCACACTGACACCTCACACGGCAGGGTATTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTTAGAAGGAAAACTAACAACCAGAAAGGACATCTACACCGAAAACCCATCTGTACATCACCATCATCAAAGACCAAAAGTAGATAAAACCACAAAGATGGGGAAAAAACAGAACAGAAAAACTGGAAACTCTAAAACGCAGAGCGCCTCTCCTCCTCCAAAGGAATGCAGTTCCTCACCAGCAACAGAACAAAGCTGGATGGAGAATGATTTTGACGAGCTGAGAGAAGAAGGCTTCAGACGATCAAATTACTCTGAGCTACGGGAGGACATTCAAACCAAAGGCAAAGAAGTTGAAAACTTTGAAAAAAATTTAGAAGAATGTATAACTAGAATAACCAATACAGAGAAGTGCTTAAAGGAGCTGATGGAGCTGAAAACCAAGGCTCGAGAACTACGTGAAGAATGCAGAAGCCTCAGGAGCCGATGCGATCAACTGGAAGAAAGGGTATCAGCAATGGAAGATGAAATGAATGAAATGAAGCGAGAAGGGAAGTTTAGAGAAAAAAGAATAAAAAGAAATGAGCAAAGCCTCCAAGAAATATGGGACTATGTGAAAAGACCAAATCTACGTCTGATTGGTGTACCTGAAAGTGATGTGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTATCCAGGAGAACTTCCCCAATCTAGCAAGGCAGGCCAACGTTCAGATTCAGGAAATACAGAGAACGCCACAAAGATACTCCTCGAGAAGAGCAACTCCAAGACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGTTAAGGGCAGCCAGAGAGAAAGGTCGGGTTACCCTCAAAGGAAAGCCCATCAGACTAACAGCGGATCTCTCGGCAGAAACCCTACAAGCCAGAAGAGAGTGGGGGCCAATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTATAGACAAGCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCCCTAAAAGAGCTCCTGAAGGAAGCGCTAAACATGGAAAGGAACAACCGGTACCAGCCGCTGCAAAATCATGCCAAAATGTAAAGACCATCGAGACTAGGAAGAAACTGCATCAACTAATGAGCAAAATCACCAGCTAACATCATAATGACAGGATCAAATTCACACATAACAATATTAACTTTAAATATAAATGGACTAAATTCTGCAATTAAAAGACACAGACTGGCAAGTTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACGTGCAGAGACACACATAGGCTCAAAATAAAAGGATGGAGGAAGATCTACCAAGCCAATGGAAAACAAAAAAAGGCAGGGGTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATCAAAAGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATTCAACAAGAGGAGCTAACTATCCTAAATATTTATGCACCCAATACAGGAGCACCCAGATTCATAAAGCAAGTCCTCAGTGACCTACAAAGAGACTTAGACTCCCACACATTAATAATGGGAGACTTTAACACCCCACTGTCAACATTAGACAGATCAACGAGACAGAAAGTCAACAAGGATACCCAGGAATTGAACTCAGCTCTGCACCAAGCAGACCTAATAGACATCTACAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTCAGCACCACACCACACCTATTCCAAAATTGACCACATAGTTGGAAGTAAAGCTCTCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTATCTCTCAGACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAATCTCACTCAAAGCCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACGAAATGAACGCAGAAATAAAGATGTTCTTTGAAACCAACAAGAACAAAGACACCACATACCAGAATCTCTGGGACGCATTCAAAGCAGTGTGTAGAGGGAAATTTATAGCACTAAATGCCTACAAGAGAAAGCAGGAAAGATCCAAAATTGACACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACACATTCAAAAGCTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGGAAATAGAGACACAAAAAACCCTTCAAAAAATCAATGAATCCAGGAGCTGGTTTTTTGAAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAAAAAAGAGAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGGATATCACCACCGATCCCACAGAAATACAAACTACCATCAGAGAATACTACAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATACATTCCTCGACACATACACTCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGTGGCAATAATCAATAGTTTACCAACCAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGTACATGGAGGAACTGGTACCATTCCTTCTGAAACTATTCCAATCAATAGAAAAAGAGGGAATCCTCCCTAACTCATTTTATGAGGCCAGCATCATTCTGATACCAAAGCCGGGCAGAGACACAACCAAAAAAGAGAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATACGCAAATCAATAAATGTAATCCAGCATATAAACAGAGCCAAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAAGCCTTTGACAAAATTCAACAACCCTTCATGCTAAAAACTCTCAATAAATTAGGTATTGATGGGACGTATTTCAAAATAATAAGAGCTATCTATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACCGGCACAAGACAGGGATGCCCTCTCTCACCGCTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGGCAGGAGAAGGAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTTGCAGACGACATGATTGTATATCTAGAAAACCCCATCGTCTCAGCCCAAAATCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAATCACAAGCATTCTTATACACCAACAACAGACAAACAGAGAGCCAAATCATGGGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAAGGAAATAAAAGAGGAGACAAACAAATGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACATCATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGACATCCCATTACTGGGTATATACCCAAATGAGTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGACCCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAA T 30 PASS SVTYPE=DEL;SVLEN=6035;RM_score=4103;RM_repeat=L1HS;RM_clsfam=LINE/L1;LCR=0.96705;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +4 167451236 . GGATATATATCCATATATTCACATATATGGATATATATCCATATATTCACATATAT G 30 PASS TRF;TRFdiff=-2;TRFrepeat=ATATATATATCCATATATTCACATATATG;TRFovl=1;TRFstart=167450892;TRFend=167451737;TRFperiod=28;TRFcopies=28;TRFscore=2031;TRFentropy=1.59;SVTYPE=DEL;SVLEN=55;LCR=0.866044;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +4 167451519 . TATATATCATATATTCACATATATGATATATATATCATATATTCACATATATGATATATATATCATATATTCACATATATG T 30 PASS TRF;TRFdiff=-2.9;TRFrepeat=ATATATATATCCATATATTCACATATATG;TRFovl=1;TRFstart=167450892;TRFend=167451737;TRFperiod=28;TRFcopies=27.1;TRFscore=2031;TRFentropy=1.59;SVTYPE=DEL;SVLEN=80;RM_score=36;RM_repeat=(TA)N;RM_clsfam=Simple_repeat;LCR=0.788549;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +4 167787682 . TATTTAATTATTTAACAAATAAATTATTTAATTATTTAACAAATAAATTATTTAATTATTTAACAAATAAATAAATTATTTAATTATTTAACAAATAAATAAATCATTTAATTATTTAACAAATAAATC T 30 PASS TRF;TRFdiff=-5.3;TRFrepeat=ATTTAAATTTAAATTTATTTATGTAAGCA;TRFovl=1;TRFstart=167787487;TRFend=167788087;TRFperiod=24;TRFcopies=17.3;TRFscore=200;TRFentropy=1.28;SVTYPE=DEL;SVLEN=128;RM_score=50;RM_repeat=(TAAT)N;RM_clsfam=Simple_repeat;LCR=0.622694;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:1,1 +4 169178281 . TAAATAAGCAACTATGCTTATTTAAAAAAATAAGCAACTATGCTTATTTAAAA T 30 PASS SVTYPE=DEL;SVLEN=52;LCR=0.833695;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +4 169357309 . CCTGTAATCCCAGCACTTTGTGAGGCTGAGGTGGGAGGATTGCTTGAGGTCTGGAGTTCGAGACTAGGCTGGGAAGCAAAGCAAGACTCTGTCTCTACAAAAATTTAAAAGTTAGCTGAACATGGTCATGTACACCTGTAGACCCAGCTACCTGAGAGGCTGAGGTGGGAGGACTGCTTGAGTCTAGGAGTTTGAGACTGCAGTGAGTCATGATTTTGCCACTGGACTCCAGCCTGTGTGACAGAGTAAAATCCTGTCTCAAAAAAAAAGAATTATTAATGAGTATGTAGAACATTGATTCCACTTCTTCAGAATGCACATTCTTTTAGGAAAAAGTATATCTCAACAAATTTTAACTAACTGGTATCATATAAAAAAAAAATCAGCAAACTATGCTGTGTAGGCCAAACCCAGCTTGCCAT C 30 PASS SVTYPE=DEL;SVLEN=421;LCR=0.98677;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +10 131377105 . C CCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCTACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTGGAGGAGCACCACGGATGAGGGAGCAT 30 PASS TRF;TRFdiff=8;TRFrepeat=GAGGAGCACCACGGATGAGGGAGCACCAGGCCCACAGGGGAGGAGGATCCTGAACCGTG;TRFovl=1;TRFstart=131376784;TRFend=131377282;TRFperiod=59;TRFcopies=16.5;TRFscore=1467;TRFentropy=1.81;TRFsim=0.996;SVTYPE=INS;SVLEN=472;LCR=0.906094;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:0,1 +10 131486818 . T TATGTGTGTTTATGCCCATGTTCACATGTGTACACTATGTGTATGTGTGTTTATGCTCATGTTTGCATGTATACATTATGTGTATGTGTGTTTATGCTCATGTTTGCATGTGTACATGTGTATGTGTGTTTATGCCCATGTTCACATGTGTACATTATGTGTATGTGTGTTTATGCCCATGTTCACATGTGTACATTATGTGTATGTGTGTTTATGCTCATGTTTGCATGTGTACATGTGTATGTGTGTTTATGCTCATGTTCACGTGTGTACATTATGTGTATGTGTTTATGCTCATGTTCGCATGTGTACATTATGTGTATGTGTGTTTATGCTCATGTTCACATGTGTACATTATGTGTATGTGTGTTTATGCCCATGTTCACACGTGTACATTATGTGTATGTGTGTTTATGCTC 30 PASS TRF;TRFdiff=10.2;TRFrepeat=TGTATGTGTGTTTATGCTCATGTTCACATGTGTACATTATG;TRFovl=1;TRFstart=131486495;TRFend=131487110;TRFperiod=41;TRFcopies=25.3;TRFscore=979;TRFentropy=1.81;TRFsim=0.925;SVTYPE=INS;SVLEN=418;LCR=0.918294;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +10 131512437 . G GTATATGTTATGTGTGTGTGGCCCCTGTGCCTTGTGCTTATGCATATGTACTGTGTGTTGTGAGTATATGTTGTGTGTGTAATGTGCATGTTGTGCATGGTGTGTATGTTGTGTACGTATGTTTATGTGTATATGCATGTGTCTTGTGTTTTGGGTGTATGTTGTGTGTATGTGTGGAGTGTATGATTTATGTGTGTGCACATATATTATGTGTTGTGGGTGCATTTTGTGTGAGTGTACATGTTGTATTGTATGTTCTATGTGTGGTGTGTAGGGCTATGTGTGTATGTTTGTGTCATGTGCGTTTTGGGTGTATGTTGTGTACATGTGTGGTGTGCATGGTTTATGTGTGTGCATATGTTATGTGTTGTGGGTGTGTGTTGTGTGTGTGCATGTGTTTTGTGTTCTTTGTGTGGTGTGTCTGTTTATGTGTGTATGTGTGTGTCATGTGTGTTTTGGGTGTGTGTTATGTATATGTGTGGTGTGTATGGTTTA 30 PASS TRF;TRFdiff=0;TRFrepeat=ATGTGTTGTGGGTGTGTGTTGTGTGTGTGCATGTGTTTATGTGTTCTTTGTGTGGTGTGTATGTTTATGTGTGTATGTGTGTGTCATGTGTGTTTTGGGTGTATGTTATGTGTATGTGTGGTGTGTATGGTTTATGTGTGTGCATATGTTGTGTGTTGTGGGTGTGTGTTGTGTGTGCATGTGTTGTATTGTATGTTCTTGTGTGGTGTGTATGTTTATGTGTGTATGTATGTGTCTTGTGCGCTTTGGGTGTATGTTATGTATATGTGTGGTGTGCATGGTTTATGTGTGTGCATATGTT;TRFovl=1;TRFstart=131512177;TRFend=131513230;TRFperiod=301;TRFcopies=3.4;TRFscore=1729;TRFentropy=1.61;SVTYPE=INS;SVLEN=494;RM_score=127;RM_repeat=(TG)N;RM_clsfam=Simple_repeat;LCR=0.823445;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 +10 131623844 . A AGAGAGGTGGGAGAGAGGTGGGGGAGAGAGGTGGGGGGAGGTGGGGGAGGGAGGTGGGGGAGAGAGGTGGGG 30 PASS TRF;TRFdiff=6.5;TRFrepeat=TGGGGGAGAGG;TRFovl=1;TRFstart=131623175;TRFend=131625010;TRFperiod=11;TRFcopies=166;TRFscore=3745;TRFentropy=1.21;TRFsim=0.922;SVTYPE=INS;SVLEN=71;LCR=0.561304;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|0:0,1 +10 131623844 . A AGAGAGGTGGGGGAGAGAGGTGGGGGGAGGTGGGGGAGGGAGGTGGGGGAGAGAGGTGGGG 30 PASS TRF;TRFdiff=0;TRFrepeat=GAGAGGTGGGG;TRFovl=1;TRFstart=131622966;TRFend=131625070;TRFperiod=11;TRFcopies=181.9;TRFscore=4278;TRFentropy=1.2;SVTYPE=INS;SVLEN=60;LCR=0.548613;STIX_ZERO=1;STIX_ONE=0;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 0|1:0,1 +10 131624691 . G GGGAGAGAGGTGGGGAAGAGGTGGGGGAGAGGTGGGGGAGAGGTGGGGGAGAGGTGGGGGGAGGTGGGGGAGAGAGAT 30 PASS TRF;TRFdiff=0;TRFrepeat=GAGAGGTGGGG;TRFovl=1;TRFstart=131622966;TRFend=131625087;TRFperiod=11;TRFcopies=183.9;TRFscore=4342;TRFentropy=1.2;SVTYPE=INS;SVLEN=77;LCR=0.579225;STIX_ZERO=0;STIX_ONE=1;STIX_QUANTS=0,0,0;STIX_QUANT_DEPTHS=0,0,0,0 GT:AD 1|1:0,2 diff --git a/stix-suite/versions/1.0.0/bin/excord b/stix-suite/versions/1.0.0/bin/excord new file mode 100755 index 0000000..125aebc Binary files /dev/null and b/stix-suite/versions/1.0.0/bin/excord differ diff --git a/stix-suite/versions/1.0.0/bin/excord-lr b/stix-suite/versions/1.0.0/bin/excord-lr new file mode 100755 index 0000000..7784e06 Binary files /dev/null and b/stix-suite/versions/1.0.0/bin/excord-lr differ diff --git a/stix-suite/versions/1.0.0/bin/giggle b/stix-suite/versions/1.0.0/bin/giggle new file mode 100755 index 0000000..2e6faed Binary files /dev/null and b/stix-suite/versions/1.0.0/bin/giggle differ diff --git a/stix-suite/versions/1.0.0/bin/stix b/stix-suite/versions/1.0.0/bin/stix new file mode 100755 index 0000000..ac82d31 Binary files /dev/null and b/stix-suite/versions/1.0.0/bin/stix differ diff --git a/stix-suite/versions/1.0.1/bin/excord b/stix-suite/versions/1.0.1/bin/excord new file mode 100755 index 0000000..125aebc Binary files /dev/null and b/stix-suite/versions/1.0.1/bin/excord differ diff --git a/stix-suite/versions/1.0.1/bin/excord-lr b/stix-suite/versions/1.0.1/bin/excord-lr new file mode 100755 index 0000000..7784e06 Binary files /dev/null and b/stix-suite/versions/1.0.1/bin/excord-lr differ diff --git a/stix-suite/versions/1.0.1/bin/giggle b/stix-suite/versions/1.0.1/bin/giggle new file mode 100755 index 0000000..2e6faed Binary files /dev/null and b/stix-suite/versions/1.0.1/bin/giggle differ diff --git a/stix-suite/versions/1.0.1/bin/stix b/stix-suite/versions/1.0.1/bin/stix new file mode 100755 index 0000000..ac82d31 Binary files /dev/null and b/stix-suite/versions/1.0.1/bin/stix differ diff --git a/stix-suite/versions/1.0.1/bin/stix-merge.py b/stix-suite/versions/1.0.1/bin/stix-merge.py new file mode 100755 index 0000000..5d2bd6b --- /dev/null +++ b/stix-suite/versions/1.0.1/bin/stix-merge.py @@ -0,0 +1,132 @@ +from collections import OrderedDict +import argparse +from copy import deepcopy +import os + +VERSION="1.0.0" + +def main(): + + parser = argparse.ArgumentParser() + parser.add_argument('-i', "--input", nargs="*", + help="input individual STIX annotated vcfs") + + parser.add_argument('-o', "--output", + help="output file") + parser.add_argument('-v', '--version', + action='version', + version=f'%(prog)s {VERSION}') + + args = parser.parse_args() + + if len(args.input) < 2: + print("please provide at least two vcf files to merge!") + exit(1) + + if os.path.exists(args.output): + answer = input(f"output file:{args.output} exists! override?[Yy/Nn]") + if answer.strip().lower() == "y": + os.remove(args.output) + else: + print("Nothing to do,exit...") + exit(0) + + for single_vcf in args.input: + if not single_vcf.strip().upper().endswith("VCF"): + print(f"Warning: detected wrong suffix in {single_vcf}") + + merged_vcf_content = OrderedDict() + merged_vcf_header = [] + clean_input = [x for x in args.input if x != args.output] + base_vcf = clean_input[0] + + + # process the first input sharded vcf file as template vcf. + count = 0 + with open(base_vcf) as baseinf: + for line in baseinf: + count += 1 + if line.startswith('#'): + merged_vcf_header.append(line) + continue + + xline = line.strip().split("\t") + uniKey = "@".join(xline[0:5]) + info_str = xline[7].split(";") + info_dict = {x.split("=")[0]: x.split("=")[1] + for x in info_str if '=' in x} + + STIX_ONE = info_dict.get("STIX_ONE", None) + STIX_ZERO = info_dict.get("STIX_ZERO", None) + if (STIX_ONE is not None) and (STIX_ZERO is not None): + merged_vcf_content[uniKey] = { + "raw_xline": deepcopy(xline), + "stix_count": [int(STIX_ZERO), int(STIX_ONE)] + } + else: + raise Exception( + f"Can not get STIX count from base vcf:{base_vcf},at line {count}") + + # iter read different vcfs and extract the STIX_ZERO and STIX_ONEs + count = 0 + for other_vcf in clean_input[1:]: + with open(other_vcf) as otherinf: + for line in otherinf: + count += 1 + if line.startswith("#"): + continue + xline = line.strip().split("\t") + uniKey = "@".join(xline[0:5]) + info_str = xline[7].split(";") + info_dict = {x.split("=")[0]: x.split("=")[1] + for x in info_str if '=' in x} + STIX_ONE = info_dict.get("STIX_ONE", None) + STIX_ZERO = info_dict.get("STIX_ZERO", None) + # print(STIX_ZERO,STIX_ONE) + if (STIX_ONE is not None) and (STIX_ZERO is not None): + # print("xx") + merged_vcf_content[uniKey]["stix_count"][0] += int(STIX_ZERO) + merged_vcf_content[uniKey]["stix_count"][1] += int(STIX_ONE) + else: + raise Exception( + f"Can not get STIX count from base vcf:{base_vcf},at line {count}") + + + # iter read different vcfs and extract the STIX_ZERO and STIX_ONEs + with open(args.output, 'w') as outf: + no_stix_freq = True + for ee in merged_vcf_header: + if "STIX_FREQ" in ee: + no_stix_freq = False + if no_stix_freq: + merged_vcf_header.insert(-1,'##INFO=\n') + for x in merged_vcf_header: + outf.write(x) + outf.flush() + for y in merged_vcf_content.values(): + raw_list = y['raw_xline'] + stix_count = y["stix_count"] + raw_info_list = raw_list[7].split(";") + # print(raw_info_list) + # print(raw_info_list,stix_count) + new_info_list = [] + + for each_info in raw_info_list: + if "STIX_ONE" in each_info: + new_info_list.append(f"STIX_ONE={stix_count[1]}") + continue + elif "STIX_ZERO" in each_info: + new_info_list.append(f"STIX_ZERO={stix_count[0]}") + continue + elif "STIX_FREQ" in each_info: + continue # do nothing + else: + new_info_list.append(each_info) + new_info_list.append(f"STIX_FREQ={stix_count[1]/(stix_count[1]+stix_count[0]) :.4f}") + raw_list[7] = ";".join(new_info_list) + out_str = '\t'.join(raw_list) + "\n" + outf.write(out_str) + + +if __name__ == "__main__": + main()