Question: Filtering multisample VCF based on genotype using SnpSift filter
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2.4 years ago by
United States
bioinforesearchquestions180 wrote:

Hi all,

I have a VCF for 20 samples. Then I extracted three samples (sample 1,23 and 46) from it. My aim is to filter "0/1, 1/1, 1/2, etc" i.e. (NonRef) from the multisample VCF file. So I used the following script to do it.

$ java -Xmx12G -jar snpEff/SnpSift.jar filter "isVariant( GEN[ * ] ) | isHet( GEN[ * ] )" WES01.WES23.WES46.recal.PASS.filtered.snpEff.exonic.vcf > WES01.WES23.WES46.recal.PASS.NonRef.filtered.snpEff.exonic.vcf

Original input VCF file: enter image description here enter image description here enter image description here enter image description here

In the input VCF file, for position "10371", sample1's genotype is "0/0", sample2's genotype is "0/1" and sample3's genotype is "1/1". Which need to be present in the output VCF file. I used "GEN[ * ] for any matches in the sample genotype. But why didn't I get it in my output VCF?

I assume, the SnpSift.jar file just looked into the first sample's genotype, which is 0/0, so it didn't include in the output VCF.

Output VCF file: enter image description here

dnaseq genotype snps snpsift vcf • 1.2k views
ADD COMMENTlink modified 2.3 years ago by RamRS19k • written 2.4 years ago by bioinforesearchquestions180

You may want to check out your images - they lead to 404s.

ADD REPLYlink written 2.3 years ago by RamRS19k

Hi Ram,

Are you able to see the images now?

ADD REPLYlink written 2.3 years ago by bioinforesearchquestions180

Nope, nothing still.

ADD REPLYlink written 2.3 years ago by RamRS19k
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