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How to filter a multisample VCF based on individual sample depth?

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

samtools mpileup vcf gbs
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updated by pascal • pascal • written by jtwalker • jtwalker

1 answer

use GATK VariantFiltration 

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

or vcffilterjs e.g: Filtering vcf file by DP

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written by Pierre Lindenbaum Pierre Lindenbaum

What about changing the genotypes of this sample (below 10) to missing instead of removing the sites completely?

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written by pascal • pascal

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