I am currently trying to filter a multi-sample vcf file obtained with samtools mpileup. I would like to keep the positions with all samples depths > 4.
I found a way with SnpSift filter, but I have to specify each sample one by one:
cat test.vcf | java -jar SnpSift.jar filter "(GEN.DP>4) & (GEN.DP>4) & ... & (GEN.DP>4)" > filtered.vcf
(i've got 66 samples ... )
Does anyone know how to apply this filtering option to all samples without specifying each samples one by one? (GEN[*] does not seem to work)
Moreover i would like to apply others genotype calling filters on subsets of my samples, is there a way to apply a filter to a specific subset?