Hi, I have run GATK Unified genotyper with multisample and I am getting unexpected output. (Hard filters used)
Here are examples of the output format I get in the vcf for a sample: 0/1:43,4:PASS:24:24,0,4368, ./.:.:PASS or 0/0:2,0:2:DPFilter:6:0,6,47 as well as 0/0:12,0:37:0,37,830. The latter is the format I would expect. What does this mean? Also I get the filter PASS even when all but two samples have ./.:.:PASS and the other two have 1/1:0,1:1:DPFilter;GQFilter:3:38,3,0 and 1/1:0,1:1:DPFilter;GQFilter:3:38,3,0.
Also I ran HalpotypeCaller multisample and get similar output all though more of the 0/0:12,0:37:0,37,830 format....