Question: How to filter a multisample VCF based on individual sample depth?
0
gravatar for jtwalker
20 months ago by
jtwalker20
jtwalker20 wrote:

I have a fairly large (800< sample) VCF file that I would like to filter based on the depth of individual aligned samples. I initially attempted to filter based on the DP field, but this seems to be the total depth at a given site, rather than the depth of an individual at that site. Does anyone know how I could accomplish this?

Thanks

gbs mpileup samtools vcf • 924 views
ADD COMMENTlink modified 20 months ago by Pierre Lindenbaum117k • written 20 months ago by jtwalker20
2
gravatar for Pierre Lindenbaum
20 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

use GATK VariantFiltration

    -select 'vc.getGenotype("SAMPLENAME").getDP() > 10'

or vcffilterjs e.g: Filtering vcf file by DP

ADD COMMENTlink written 20 months ago by Pierre Lindenbaum117k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 695 users visited in the last hour