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GATK HC joint call gives multiple lines for same variant
I was doing some QC and happen to see the following behavior that are not what i wanted/expected:
chr4 151267927 . A C 43.77 PASS AC=50;AF=0.532;AN=94;DP=739 GT:AD:DP:GQ:PGT:PID:PL ...
chr4 151267927 . A AC,AAC 43.77 PASS AC=6,1;AF=0.429,0.071;AN=14;DP=97;MLEAC=1;MLEAF=0.500 ...
chr4 151267927 . A C,AC 426.77 PASS AC=105,4;AF=0.491,0.019;AN=214;DP=1815 GT:DP:GQ:PGT:PID
This would be fine until i perform variant selection, e.g. select SNP/INDEL will both missing the third line.
I am using GATK 3.4 (GenotypeGVCFs,Version=3.4-0-g7e26428)
The VCF is merged from 2000 samples, NOT joint genotyping.
Any way to fix this using GATK? hope i am not missing anything.