Hello, I'd like to filter for sites that have a DP>5 in my normal sample and DP>10 in the tumor. My vcf has two samples columns, TUMOR NORMAL. How do I do that with a bcftools expression? I see in the documentation how to apply the filter for one or all samples in a vcf row but I couldn't find a way to specify the sample name. Thanks a lot.
Hava a look at SnpSift filter.
With SnpSift you can build any expression that evaluates to TRUE / FALSE using the attributes of the variant and or the attributes of one or more specific samples.
cat my.vcf | java -jar SnpSift.jar filter "GEN.DP > 5 && GEN.DP > 10"
variant.getGenotype("NORMAL").getDP() > 5 && variant.getGenotype("TUMOR").getDP() > 10