Filtering multisample VCF based on genotype using SnpSift filter
0
0
Entering edit mode
5.9 years ago

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

VCF snpSift genotype DNASeq snps • 2.6k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Hi Ram,

Are you able to see the images now?

ADD REPLY
0
Entering edit mode

Nope, nothing still.

ADD REPLY

Login before adding your answer.

Traffic: 848 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6