filtering multi sample vcf file
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7 weeks ago
maajid • 0

Hello all ,

I have a multi sample vcf file of 1000 individuals for one gene . Some of the samples do not have any variants in them like "0/0".I want to filter them out and keep only the samples with variants associated like "0/1" and "1/1".How can I do this .Kindly give a command and tool for the same .

vcf filtering file • 697 views
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you could use bcftools view for that, check the doc here: http://samtools.github.io/bcftools/bcftools.html#view

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Thanks you .What command should I precisely use from that ?

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7 weeks ago

using http://lindenb.github.io/jvarkit/VcfFilterJdk.html

 java -jar dist/vcffilterjdk.jar -e 'final Set<String> samples=new HashSet<>(Arrays.asList("S2","S3")); return samples.stream().map(S->variant.getGenotype(S)).allMatch(G->G.isHet() || G.isHomVar()) && variant.getGenotypes().stream().filter(G->!samples.contains(G.getSampleName())).noneMatch(G->G.isHet() || G.isHomVar());'  in.vcf.gz
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I installed the tool and ran the command above but it showing some errors like "java.lang.RuntimeException: Cannot compile" and is not producing any output.

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show me the command and the complet stack trace

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git clone "https://github.com/lindenb/jvarkit.git"
cd jvarkit
./gradlew vcffilterjdk

java -jar dist/vcffilterjdk.jar -e 'final Set<String> samples=new HashSet<>(Arrays.asList("S2","S3")); return samples.stream().map(S->variant.getGenotype(S)).allMatch(G->G.isHet() || G.isHomVar()) && variant.getGenotypes().stream().filter(G->!samples.contains(G.getSampleName())).noneMatch(G->G.isHet() || G.isHomVar());'  aqp1.1000g.vcf.gz
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S2 and S3 should be your sample names...

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I have vcf file wth 1000 samples and i need only those samples which contain variants like 0/1 ,1/0 and 1/1 and remove samples with 0/0 . so what should I write in place of s1 and s2

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Ah, so your question was not clear to me ; You cannot remove samples from a VCF file for one variant and not for the other variants of the file.

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Thank you . Now I have annotated multi sample vcf file using snpEff . How can I filter exonic variants in the separate file and intronic as well as other UTRs in separate file .which command can I use to separate out exonic variants .

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this is unrelated to your original question.

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