How to filter a multisample VCF based on individual sample depth?
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4.1 years ago
jtwalker ▴ 20

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 • 2.0k views
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4.1 years ago

use GATK VariantFiltration

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

or vcffilterjs e.g: Filtering vcf file by DP

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

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