getting started?

[biocyberman]

Hi
VisCap seems to be an interesting tool. I want to try it out but am still not clear how to start.

The first question is: What is the exact command of gatk DepthOfCoverage should I run? There are many options to it as you may see.

So a sample command that your team used can be a good reference.

Secondly, some more details will help a lot:

1. What is the requirements for the BED to use with GATK.
2. What kind of samples are usable with VisCap? I have gene panel data captured by bait/probe hybridization and sequenced with Ion Proton. Is it usable with VisCap?
3. At minimum, how many control samples are required?
4. Do I need to remove duplicates before running GATK and VisCap?

Your answers will be much appreciated.

Kind regards
Vang

[dharbi]

A - The exact option to use for GATK DepthOfCoverage is not important. The most important, however, is to use the same option for all your outputs.
B-

1. Usual bed file without overlapping intervals
   Note that VisCap takes interval list file and not a bed file
2. VisCap is designed to run on normal batches (germline samples). It has been designed for hybrid-capture panels, although tested as well on amplicon-based ones. The sequencer is not important, however the same platform should be used
3. There is no minimum (but not 0!), the more you put the better.
4. Again removing or not removing duplicates is your choice, however, all the samples should be processed the same way (i.e., cannot compare a sample which duplicates were removed to control samples which duplicates were not removed, since duplication removal affects coverage which VisCap relies on to infer copy number calls)

Best
Djamel

[rframal]

Hi,

I am testing the VisCap. It is working fine but I can not get the gene(exon) name in the file "cnv_boxplot_outliers.xls".

My interval file looks like the following:

@hd VN:1.5 SO:coordinate
@sq SN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr1 LN:249250621 M5:1b22b98cdeb4a9304cb5d48026a85128 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr2 LN:243199373 M5:a0d9851da00400dec1098a9255ac712e UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr3 LN:198022430 M5:641e4338fa8d52a5b781bd2a2c08d3c3 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr4 LN:191154276 M5:23dccd106897542ad87d2765d28a19a1 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr5 LN:180915260 M5:0740173db9ffd264d728f32784845cd7 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr6 LN:171115067 M5:1d3a93a248d92a729ee764823acbbc6b UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr7 LN:159138663 M5:618366e953d6aaad97dbe4777c29375e UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr8 LN:146364022 M5:96f514a9929e410c6651697bded59aec UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr9 LN:141213431 M5:3e273117f15e0a400f01055d9f393768 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr10 LN:135534747 M5:988c28e000e84c26d552359af1ea2e1d UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr11 LN:135006516 M5:98c59049a2df285c76ffb1c6db8f8b96 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr12 LN:133851895 M5:51851ac0e1a115847ad36449b0015864 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr13 LN:115169878 M5:283f8d7892baa81b510a015719ca7b0b UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr14 LN:107349540 M5:98f3cae32b2a2e9524bc19813927542e UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr15 LN:102531392 M5:e5645a794a8238215b2cd77acb95a078 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr16 LN:90354753 M5:fc9b1a7b42b97a864f56b348b06095e6 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr18 LN:78077248 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr19 LN:59128983 M5:1aacd71f30db8e561810913e0b72636d UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr20 LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr21 LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chr22 LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chrX LN:155270560 M5:7e0e2e580297b7764e31dbc80c2540dd UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
@sq SN:chrY LN:59373566 M5:1fa3474750af0948bdf97d5a0ee52e51 UR:file:/data1/ref/Homo_sapiens.GRCh37.75.genome.fa
chr1 10292320 10292502 + KIF1B
chr1 10316296 10316391 + KIF1B
chr1 10318542 10318740 + KIF1B

Is this the correct interval file format ? Could you please show me an example of the corrected interval file ?

Best,

Rodrigo

[luckyluke95]

Dear Rodrigo and Djamel.

Sorry for this post in this old issue but I am trying to run Viscap and have a lot of error messages.
I'm trying to check if all my input files are ok but I saw here this post :
"Usual bed file without overlapping intervals
Note that VisCap takes interval list file and not a bed file"
It is said use a bed file but not a bed file ?????!!!
Could you help me about that ?
If I use a .bed file without overlapping region, is the classical format ok ?
Thanks in advance for your help.

Abou