Question: How To Filter Vcf By Coverage?
0
gravatar for newDNASeqer
6.3 years ago by
newDNASeqer680
United States
newDNASeqer680 wrote:

I used GATK to make variant calling on an exome-seq data set that has 10 samples. I copied one line (for an SNP identified) from the VCF output as shown below. The genotype is indicated (for example 0/1 for heterozygous mutant). The reference and variant reads are shown immediately after the genotype 0/1 (for example).

My question is how do you filter the VCF by the coverage (ref reads + variant reads ?). What to do if some of the samples pass the filtration and other samples fail to pass?

0/1:2,10:12:28:256,0,28    0/1:13,18:31:99:427,0,315    0/1:6,9:15:99:246,0,155    0/1:8,8:16:99:176,0,187    0/0:8,0:8:24:0,24,259    0/1:5,6:11:99:144,0,136    0/1:5,5:10:99:103,0,110    0/1:4,6:10:99:161,0,103    0/0:10,0:10:30:0,30,277    0/1:16,7:23:99:192,0,529
vcf coverage • 5.3k views
ADD COMMENTlink modified 3.0 years ago by aadeokar0 • written 6.3 years ago by newDNASeqer680

Hi Pierre, Could you please inform me how i can filter my multi-sample vcf file (250 samples) for only variants with at five homozygous REF and five homozygous ALT call using VCFFilterJS. Thank you !

ADD REPLYlink written 3.0 years ago by aadeokar0

this is a new question, please open this as a new question: https://www.biostars.org/p/new/post/

ADD REPLYlink written 3.0 years ago by Pierre Lindenbaum129k

Could you please inform me how i can filter my multi-sample vcf (250 samples) file for only variants with at least five homozygous REF and five homozygous ALT call using VCFFilterJS.

ADD REPLYlink written 3.0 years ago by aadeokar0

again, I'll give you the answer, but please, askthis a different question ( https://www.biostars.org/p/new/post/ ) (it's not How To Filter Vcf By Coverage? ). Ask your question as a NEW question. So everybody can contribute and follow the new thread. Thanks.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Pierre Lindenbaum129k
1
gravatar for Raony Guimarães
6.3 years ago by
Dublin / Ireland
Raony Guimarães1.1k wrote:

You could use the parameter "--max-indv-meanDP" from vcftools.

--max-indv-meanDP <float> Calculate the mean coverage on a per-individual basis. Only individuals with coverage within the range specified by these options are included in subsequent analyses.

Source: http://manpages.ubuntu.com/manpages/trusty/man1/vcftools.1.html

ADD COMMENTlink written 6.3 years ago by Raony Guimarães1.1k

thanks, but I found the latest version of vcftools does not support --max-indv-meanDP http://vcftools.sourceforge.net/man_latest.html

ADD REPLYlink written 6.3 years ago by newDNASeqer680
1
gravatar for Pierre Lindenbaum
6.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

I wrote a tool VCFFilterJS to filter a VCF file with a javascript program/expression.

See https://github.com/lindenb/jvarkit/wiki/VCFFilterJS and A: GATK multi-sample VCF VariantFiltration for an example.

ADD COMMENTlink modified 6 months ago by RamRS27k • written 6.3 years ago by Pierre Lindenbaum129k
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