Question: How to filter a multisample VCF based on individual sample depth?
0
gravatar for jtwalker
2.8 years 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 • 1.4k views
ADD COMMENTlink modified 2.8 years ago by Pierre Lindenbaum127k • written 2.8 years ago by jtwalker20
2
gravatar for Pierre Lindenbaum
2.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

use GATK VariantFiltration

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

or vcffilterjs e.g: Filtering vcf file by DP

ADD COMMENTlink written 2.8 years ago by Pierre Lindenbaum127k
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