I have 4 libraries with multiple sequencing runs per library. I called the variants for each run individually and then combined them using GATK's CombineVariants as well as CatVariants procedure.
NW_006711278.1 526153 . T C 199 . AC=2;AN=2;DP=7;DP4=0,0,3,4;MQ=60;MQ0F=0;MQSB=1.01283;SGB=-0.636426;VDB=0.792147;TYPE=snp GT:PL 1/1:226,21,0
NW_006711278.1 526153 . T C 172 . AC=2;AN=2;DP=6;DP4=0,0,4,2;MQ=60;MQ0F=0;MQSB=1;SGB=-0.616816;VDB=0.954032;TYPE=snp GT:PL 1/1:199,18,0
NW_006711278.1 526153 . T C 228 . AC=2;AN=2;DP=9;DP4=0,0,5,4;MQ=60;MQ0F=0;MQSB=0.974597;SGB=-0.662043;VDB=0.0292194;TYPE=snp GT:PL 1/1:255,27,0
For example above, for the same position I can see that multiple libraries have been put here. Is there any way to collapse them?
The only reason I wasn't using a large bam file containing all of these libraries was that it was taking too much time to crunch and I had a power failure and didn't want to start it all over again.
Edit: removed ambiguity, power failure overnight and the backup didn't kick in, not a segfault.