I used GATK to make variant calling on an exome-seq data set that has 10 samples. I copied one line (for an SNP identified) from the VCF output as shown below. The genotype is indicated (for example 0/1 for heterozygous mutant). The reference and variant reads are shown immediately after the genotype 0/1 (for example).
My question is how do you filter the VCF by the coverage (ref reads + variant reads ?). What to do if some of the samples pass the filtration and other samples fail to pass?
0/1:2,10:12:28:256,0,28 0/1:13,18:31:99:427,0,315 0/1:6,9:15:99:246,0,155 0/1:8,8:16:99:176,0,187 0/0:8,0:8:24:0,24,259 0/1:5,6:11:99:144,0,136 0/1:5,5:10:99:103,0,110 0/1:4,6:10:99:161,0,103 0/0:10,0:10:30:0,30,277 0/1:16,7:23:99:192,0,529