SNPSift countRef() on a VCF with missing values
1
0
Entering edit mode
4 weeks ago
FJK • 0

Hi,

I'd like to use SNPSift Filter for filtering a VCF. I found that missing value for the genotype (GT), i.e., ./., are counted as reference.

Here is a minimal example:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  sample
XXX 999 .   A   G   100 .   .   GT:PL:DP:AD:GQ  ./.:0,0,0:1:0,1:127

Here is the filter that I apply: countRef()>0

I would expect that no line passes the filter, but it returns the line although there is no call for the reference (0/0).

Does anybody have an idea?

I used SNPSift version SnpSift 4.3t on my own galaxy server and also tested usegalaxy.eu. Both give the same result.

Best regards,
Jens

SNPSift • 260 views
ADD COMMENT
0
Entering edit mode
4 weeks ago

Use

bcftools view -i 'COUNT (GT="RR")>0' in.vcf
ADD COMMENT

Login before adding your answer.

Traffic: 2528 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