Index error

[Tgrandis2025]

I am testing whether I can get (partial) haplotype reconstructed from Illumina short reads derived from a diploid heterozygous tree genome.
I generated a vcf file with freeBayes after mapping the reads to a reference genome for just one scaffold, 5.5 Mb long. pHapCompass can generate the .frag file within a few seconds, but when it comes to the actual haplotyping I get an error message.

2026-01-25 21:33:27,904 | INFO | Inferring ploidy from VCF: /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes.vcf
2026-01-25 21:33:27,904 | INFO | Inferred ploidy: 2
2026-01-25 21:33:27,912 | INFO | No fragment file provided. Will generate using extractHAIRS at: /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.frag
Using extractHAIRS binary: /home/dfbs_user/pHapCompass/src/phapcompass/bin/extractHAIRS
Running: /home/dfbs_user/pHapCompass/src/phapcompass/bin/extractHAIRS --bam /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.bam --VCF /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes.vcf --out /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.frag --mbq 13

Extracting haplotype informative reads from bamfiles /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.bam minQV 13 minMQ 20 maxIS 1000

VCF file /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes.vcf has 1686 variants
adding chrom scaffold48_cov80 to index
vcffile /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes.vcf chromosomes 1 hetvariants 1082 1686
reading sorted bamfile /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.bam
processing reads mapped to chrom "scaffold48_cov80"
final cleanup of fragment list: 11618 current chrom (null) 0 prev 0

✓ Fragment file created successfully: /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.frag
2026-01-25 21:33:29,183 | INFO | Data type: short
2026-01-25 21:33:29,183 | INFO | Result path: /home/dfbs_user/Results/Tg2_scaffold48_haplotypes
2026-01-25 21:33:29,183 | INFO | Running short-read model with mw=10.0000, lw=1.0000, sw=1.0000
Traceback (most recent call last):
File "/home/dfbs_user/conda/bin/phapcompass", line 7, in
sys.exit(main())
^^^^^^
File "/home/dfbs_user/pHapCompass/src/phapcompass/cli.py", line 126, in main
run_pHapCompass_short(args)
File "/home/dfbs_user/pHapCompass/src/phapcompass/run_pHapCompass_short.py", line 54, in run_pHapCompass_short
gi = g_per_snp[col_to_snp[nodes_cols[:, 0]]] # g at SNP position for col_i
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 1681 is out of bounds for axis 0 with size 1681

OS Linux Ubuntu 24.04.3 LTS
Python 3.12

wc -l ./Results/Tg2_vs_TgS01_scaffold48_sorted.frag
3763 ./Results/Tg2_vs_TgS01_scaffold48_sorted.frag

[Marjan-Hosseini]

Can you run pHapCompass with the --verbose flag to get more debugging information? Also, could you share:

The first few lines of your fragment file (to see the SNP indices)
The output of: grep -v "^#" your.vcf | head -20

This will help me pinpoint exactly where the index mismatch is occurring.

[Tgrandis2025]

here is the --verbose output. phapcompass --data-type short --bam-path ~/Results/Tg2_vs_TgS01_scaffold48_sorted.bam --vcf-path ~/Results/Tg2_scaffold48_FreeBayes_SNP.vcf --result-path ~/Results/Tg2_scaffold48_Freebayes_haplotypes --verbose 2026-02-03 09:02:13,959 | INFO | Inferring ploidy from VCF: /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes_SNP.vcf 2026-02-03 09:02:13,960 | INFO | Inferred ploidy: 2 2026-02-03 09:02:14,047 | INFO | No fragment file provided. Will generate using extractHAIRS at: /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.frag Using extractHAIRS binary: /home/dfbs_user/pHapCompass/src/phapcompass/bin/extractHAIRS Running: /home/dfbs_user/pHapCompass/src/phapcompass/bin/extractHAIRS --bam /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.bam --VCF /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes_SNP.vcf --out /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.frag --mbq 13 Extracting haplotype informative reads from bamfiles /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.bam minQV 13 minMQ 20 maxIS 1000 VCF file /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes_SNP.vcf has 11032 variants adding chrom scaffold48_cov80 to index vcffile /home/dfbs_user/Results/Tg2_scaffold48_FreeBayes_SNP.vcf chromosomes 1 hetvariants 11024 11032 reading sorted bamfile /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.bam processing reads mapped to chrom "scaffold48_cov80" cleaning buffer: current chrom scaffold48_cov80 position 4585167 fragments 100000 final cleanup of fragment list: 8518 current chrom (null) 0 prev 0 ✓ Fragment file created successfully: /home/dfbs_user/Results/Tg2_vs_TgS01_scaffold48_sorted.frag 2026-02-03 09:02:16,022 | INFO | Data type: short 2026-02-03 09:02:16,022 | INFO | Result path: /home/dfbs_user/Results/Tg2_scaffold48_Freebayes_haplotypes 2026-02-03 09:02:16,023 | INFO | Running short-read model with mw=10.0000, lw=1.0000, sw=1.0000 Traceback (most recent call last): File "/home/dfbs_user/conda/bin/phapcompass", line 7, in <module> sys.exit(main()) ^^^^^^ File "/home/dfbs_user/pHapCompass/src/phapcompass/cli.py", line 126, in main run_pHapCompass_short(args) File "/home/dfbs_user/pHapCompass/src/phapcompass/run_pHapCompass_short.py", line 54, in run_pHapCompass_short gi = g_per_snp[col_to_snp[nodes_cols[:, 0]]] # g at SNP position for col_i ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ IndexError: index 10854 is out of bounds for axis 0 with size 10847 It could be an error specific to vcf files generated by the FreeBayes programme/ Here are the first 20 lines of the vcf file scaffold48_cov80 35 . T C 142.691 . AB=0.727273;ABP=7.94546;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=20.3821;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.55924;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=306;QR=119;RO=3;RPL=0;RPP=20.3821;RPPR=9.52472;RPR=8;RUN=1;SAF=8;SAP=20.3821;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:3,8:3:119:8:306:-24.5831,0,-7.78317 scaffold48_cov80 43 . T C 132.009 . AB=0.538462;ABP=3.17734;AC=1;AF=0.5;AN=2;AO=7;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=18.2106;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.4194;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=286;QR=228;RO=6;RPL=0;RPP=18.2106;RPPR=16.0391;RPR=7;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=6;SRP=16.0391;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:13:6,7:6:228:7:286:-22.2014,0,-16.9654 scaffold48_cov80 72 . A T 214.638 . AB=0.578947;ABP=4.03889;AC=1;AF=0.5;AN=2;AO=11;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=26.8965;EPPR=18.2106;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.7397;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=442;QR=273;RO=7;RPL=0;RPP=26.8965;RPPR=18.2106;RPR=11;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=7;SRP=18.2106;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:19:7,11:7:273:11:442:-34.3135,0,-19.1131 scaffold48_cov80 113 . C T 403.937 . AB=0.666667;ABP=8.80089;AC=1;AF=0.5;AN=2;AO=16;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=3.0103;EPPR=5.80219;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.939;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=635;QR=273;RO=7;RPL=8;RPP=3.0103;RPPR=5.80219;RPR=8;RUN=1;SAF=16;SAP=37.7539;SAR=0;SRF=7;SRP=18.2106;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:24:7,16:7:273:16:635:-50.1582,0,-17.608 scaffold48_cov80 169 . C T 30.7322 . AB=0.208333;ABP=20.744;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=6.91895;EPPR=8.61041;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.07551;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=196;QR=735;RO=19;RPL=4;RPP=6.91895;RPPR=5.8675;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=18;SRP=36.0395;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:24:19,5:19:735:5:196:-10.7867,0,-59.2396 scaffold48_cov80 188 . T G 136.236 . AB=0.388889;ABP=4.9405;AC=1;AF=0.5;AN=2;AO=7;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.80219;EPPR=12.6832;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.3696;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=269;QR=425;RO=11;RPL=4;RPP=3.32051;RPPR=12.6832;RPR=3;RUN=1;SAF=6;SAP=10.7656;SAR=1;SRF=11;SRP=26.8965;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:18:11,7:11:425:7:269:-19.1497,0,-33.1771 scaffold48_cov80 328 . T C 238.129 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=10;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.8312;PAIRED=0.9;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=383;QR=392;RO=10;RPL=4;RPP=3.87889;RPPR=6.48466;RPR=6;RUN=1;SAF=3;SAP=6.48466;SAR=7;SRF=4;SRP=3.87889;SRR=6;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:20:10,10:10:392:10:383:-28.795,0,-29.6097 scaffold48_cov80 337 . C T 109.032 . AB=0.28;ABP=13.5202;AC=1;AF=0.5;AN=2;AO=7;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=3.32051;EPPR=4.9405;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.1056;PAIRED=0.857143;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=270;QR=716;RO=18;RPL=4;RPP=3.32051;RPPR=15.074;RPR=3;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=9;SRP=3.0103;SRR=9;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:25:18,7:18:716:7:270:-17.1355,0,-57.235 scaffold48_cov80 344 . AA AG 166.256 . AB=0.296296;ABP=12.7417;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1M1X;DP=27;DPB=27;DPRA=0;EPP=4.09604;EPPR=7.18621;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.523;PAIRED=0.875;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=319;QR=484;RO=13;RPL=4;RPP=3.0103;RPPR=4.51363;RPR=4;RUN=1;SAF=1;SAP=12.7819;SAR=7;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:27:13,8:13:484:8:319:-22.367,0,-37.1874 scaffold48_cov80 362 . T C 339.117 . AB=0.454545;ABP=3.60252;AC=1;AF=0.5;AN=2;AO=15;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=3.15506;EPPR=15.074;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=78.0847;PAIRED=0.933333;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=547;QR=691;RO=18;RPL=5;RPP=6.62942;RPPR=4.9405;RPR=10;RUN=1;SAF=5;SAP=6.62942;SAR=10;SRF=11;SRP=4.9405;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:33:18,15:18:691:15:547:-39.6126,0,-52.5769 scaffold48_cov80 367 . T A 330.326 . AB=0.433333;ABP=4.16842;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=3.17734;EPPR=24.5973;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.0603;PAIRED=0.923077;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=529;QR=603;RO=17;RPL=3;RPP=11.1951;RPPR=4.1599;RPR=10;RUN=1;SAF=5;SAP=4.51363;SAR=8;SRF=10;SRP=4.1599;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:30:17,13:17:603:13:529:-38.9249,0,-45.535 scaffold48_cov80 431 . T C 484.868 . AB=0.487179;ABP=3.06598;AC=1;AF=0.5;AN=2;AO=19;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=8.61041;EPPR=8.61041;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=98.7744;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=729;QR=671;RO=19;RPL=11;RPP=4.03889;RPPR=5.8675;RPR=8;RUN=1;SAF=8;SAP=4.03889;SAR=11;SRF=12;SRP=5.8675;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:39:19,19:19:671:19:729:-54.346,0,-49.1085 scaffold48_cov80 443 . T C 567.225 . AB=0.536585;ABP=3.48696;AC=1;AF=0.5;AN=2;AO=22;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=9.32731;EPPR=16.8392;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5789;NS=1;NUMALT=1;ODDS=100.7;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=830;QR=700;RO=19;RPL=11;RPP=3.0103;RPPR=4.03889;RPR=11;RUN=1;SAF=12;SAP=3.40511;SAR=10;SRF=13;SRP=8.61041;SRR=6;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:19,22:19:700:22:830:-62.6532,0,-50.9455 scaffold48_cov80 459 . T C 0.0468695 . AB=0.15;ABP=45.5712;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=16.0391;EPPR=9.39698;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7647;NS=1;NUMALT=1;ODDS=4.52354;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=225;QR=1214;RO=34;RPL=4;RPP=4.45795;RPPR=3.0103;RPR=2;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=23;SRP=12.2071;SRR=11;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:40:34,6:34:1214:6:225:-8.55886,0,-97.4666 scaffold48_cov80 473 . A G 559.613 . AB=0.547619;ABP=3.83753;AC=1;AF=0.5;AN=2;AO=23;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=14.4341;EPPR=12.2676;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.431;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=837;QR=698;RO=19;RPL=10;RPP=3.86001;RPPR=3.12459;RPR=13;RUN=1;SAF=15;SAP=7.63648;SAR=8;SRF=12;SRP=5.8675;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:42:19,23:19:698:23:837:-62.9726,0,-50.4695 scaffold48_cov80 486 . G A 196.512 . AB=0.268293;ABP=22.1298;AC=1;AF=0.5;AN=2;AO=11;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=3.20771;EPPR=5.61607;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.2486;PAIRED=0.909091;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=432;QR=1122;RO=30;RPL=6;RPP=3.20771;RPPR=7.64277;RPR=5;RUN=1;SAF=8;SAP=7.94546;SAR=3;SRF=17;SRP=4.16842;SRR=13;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:30,11:30:1122:11:432:-26.881,0,-88.9094 scaffold48_cov80 488 . G A 5.16773e-09 . AB=0.102564;ABP=56.5176;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=6.05036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.5494;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=1377;RO=35;RPL=0;RPP=11.6962;RPPR=3.56868;RPR=4;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=21;SRP=6.05036;SRR=14;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:39:35,4:35:1377:4:152:-2.30878,0,-112.435 scaffold48_cov80 490 . G A 13.9916 . AB=0.15;ABP=45.5712;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=4.45795;EPPR=9.39698;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.18097;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=246;QR=1321;RO=34;RPL=3;RPP=3.0103;RPPR=9.39698;RPR=3;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=22;SRP=9.39698;SRR=12;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:40:34,6:34:1321:6:246:-10.4789,0,-107.098 scaffold48_cov80 507 . TGGGT TGGGC 1036.84 . AB=0.783784;ABP=28.8919;AC=1;AF=0.5;AN=2;AO=29;CIGAR=4M1X;DP=37;DPB=37;DPRA=0;EPP=3.68421;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=0;NS=1;NUMALT=2;ODDS=15.6348;PAIRED=0.965517;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1109;QR=0;RO=0;RPL=13;RPP=3.68421;RPPR=0;RPR=16;RUN=1;SAF=17;SAP=4.88226;SAR=12;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL ./1:37:0,7,29:0:0:29:1109:-114.101,-23.1249,-14.395 scaffold48_cov80 576 . CAGG CAGA 1106.1 . AB=0.790698;ABP=34.5724;AC=1;AF=0.5;AN=2;AO=34;CIGAR=3M1X;DP=43;DPB=43;DPRA=0;EPP=3.26577;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=0;NS=1;NUMALT=2;ODDS=9.55306;PAIRED=0.970588;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1244;QR=0;RO=0;RPL=19;RPP=4.03217;RPPR=0;RPR=15;RUN=1;SAF=27;SAP=28.557;SAR=7;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL ./1:43:0,7,34:0:0:34:1244:-124.652,-23.0637,-12.8287

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On Tue, 3 Feb 2026 at 01:30, Marjan Hosseini ***@***.***> wrote: *Marjan-Hosseini* left a comment (bayesomicslab/pHapCompass#1) <#1 (comment)> Can you run pHapCompass with the --verbose flag to get more debugging information? Also, could you share: The first few lines of your fragment file (to see the SNP indices) The output of: grep -v "^#" your.vcf | head -20 This will help me pinpoint exactly where the index mismatch is occurring. — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/B3TA6NZMB7EFUEYIA672WX34J6CTBAVCNFSM6AAAAACS2JKXFWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQMZWGY2DQNBUG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Marjan-Hosseini]

Issue: Multiallelic Variants in VCF

Your FreeBayes VCF contains multiallelic variants (sites with multiple ALT alleles), which is causing the IndexError. As mentioned in our paper, pHapCompass only supports biallelic SNP sites (one REF, one ALT).

Looking at your VCF, you have variants like:

scaffold48_cov80 507 . TGGGT TGGGC ... GT ./1 ...

The genotype ./1 indicates multiple ALT alleles at this position.

Solution

Filter your VCF to keep only biallelic SNPs:

# Using bcftools (recommended)
bcftools view -m2 -M2 -v snps \
  ~/Results/Tg2_scaffold48_FreeBayes_SNP.vcf \
  -Oz -o ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.vcf.gz

bcftools index ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.vcf.gz

# Run pHapCompass
phapcompass --data-type short \
  --bam-path ~/Results/Tg2_vs_TgS01_scaffold48_sorted.bam \
  --vcf-path ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.vcf.gz \
  --result-path ~/Results/Tg2_scaffold48_Freebayes_haplotypes

Alternative (if you don't have bcftools):

# Using vcftools
vcftools --vcf ~/Results/Tg2_scaffold48_FreeBayes_SNP.vcf \
  --min-alleles 2 --max-alleles 2 --remove-indels \
  --recode --recode-INFO-all \
  --out ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic

bgzip ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.recode.vcf
tabix -p vcf ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.recode.vcf.gz

This will resolve the error. Let me know if you need any clarification!

[Tgrandis2025]

OK... it is a problem with the FreeBayes programme. The SNPs are actually all biallelic but for some of them FreeBayes calls them in a strange way, including some of the surrounding nucleotides. Admixture also complained about "half-genotypes" in the FreeBayes-generated vcf files. I resolved that in PLINK by including the filter --vcf-half-call missing. Using the m=2, M=2 filters is not going to remove them as only 2 alleles are listed. I have to search for a different solution to filter out the ./1 genotype calls from the FreeBayes output.

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On Tue, 3 Feb 2026 at 10:44, Marjan Hosseini ***@***.***> wrote: *Marjan-Hosseini* left a comment (bayesomicslab/pHapCompass#1) <#1 (comment)> Issue: Multiallelic Variants in VCF Your FreeBayes VCF contains *multiallelic variants* (sites with multiple ALT alleles), which is causing the IndexError. As mentioned in our paper, pHapCompass only supports *biallelic SNP sites* (one REF, one ALT). Looking at your VCF, you have variants like: scaffold48_cov80 507 . TGGGT TGGGC ... GT ./1 ... The genotype ./1 indicates multiple ALT alleles at this position. Solution Filter your VCF to keep only biallelic SNPs: # Using bcftools (recommended) bcftools view -m2 -M2 -v snps \ ~/Results/Tg2_scaffold48_FreeBayes_SNP.vcf \ -Oz -o ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.vcf.gz bcftools index ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.vcf.gz # Run pHapCompass phapcompass --data-type short \ --bam-path ~/Results/Tg2_vs_TgS01_scaffold48_sorted.bam \ --vcf-path ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.vcf.gz \ --result-path ~/Results/Tg2_scaffold48_Freebayes_haplotypes *Alternative (if you don't have bcftools):* # Using vcftools vcftools --vcf ~/Results/Tg2_scaffold48_FreeBayes_SNP.vcf \ --min-alleles 2 --max-alleles 2 --remove-indels \ --recode --recode-INFO-all \ --out ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic bgzip ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.recode.vcf tabix -p vcf ~/Results/Tg2_scaffold48_FreeBayes_SNP.biallelic.recode.vcf.gz This will resolve the error. Let me know if you need any clarification! — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/B3TA6N36QUPLSBB3D5RA6MD4KADRHAVCNFSM6AAAAACS2JKXFWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQMZYG4YDENZYGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>