I tried to run multi sample GATK unified genotyper (as it is better than 30x1, on each bam). I have paired samples (tumor/normal) looking for somatic variants only. I thought that GATK would return coverage, number of alternating alleles, number of reference alleles (AB,AC,AF,AN values for each sample) per each sample in a separate column, but AB,AC,AF,AN flags seem to be pooled together, based on all samples. Do I have to run GATK unifiedgenotyper to get these on a individual sample basis ? If yes, which QUALITY flag shall I use, pooled or individual ?
Thanks!
Thanks!