Hi All,
I have a multi-sample VCF file produced by the GATK Unified Genotyper. I need to now filter these variants for SNPs that have a DP < 10. However the DP entry in the info field for a multi-sample VCF is the depth across all samples. so very few variants will fail this filter and there will be many variants with low depth marked as a pass. Does anyone know of a GATK option to filter on the depth of the samples themselves. Of course, this presents another problem. How to resolve a variant that has low coverage in one individual and high coverage in another? The following is probably not possible in GATK but perhaps one could say if the largest depth across all samples is <10 or maybe if more than 10% of the samples have DP less than 10? Does it even make sense to do this?
Cheers,
Davy.
I have a multi-sample VCF file produced by the GATK Unified Genotyper. I need to now filter these variants for SNPs that have a DP < 10. However the DP entry in the info field for a multi-sample VCF is the depth across all samples. so very few variants will fail this filter and there will be many variants with low depth marked as a pass. Does anyone know of a GATK option to filter on the depth of the samples themselves. Of course, this presents another problem. How to resolve a variant that has low coverage in one individual and high coverage in another? The following is probably not possible in GATK but perhaps one could say if the largest depth across all samples is <10 or maybe if more than 10% of the samples have DP less than 10? Does it even make sense to do this?
Cheers,
Davy.
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