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A potential bug report
Dear GATK team,
I recently received a vcf file for an exome sequencing project from Broad. I found some samples were called as HET although all DP came from alternative allele. For example:
On rs1129808 (ref:A; alt:C) , I found 0/1:0,4:4:99:333,0,631 for sample 001
On chr21:33733468 (ref:A; alt:AAAAGAAAGAAAGAAAGAAAG,AAAAGAAAGAAAGAAAG,AAAAG,AAAAGAAAGAAAG,AAAAGAAAG,AAAGAAAGAAAGAAAG) , I found 0/1:0,10,0,0,0,0,0:10:5:367,0,5,400,35,434,400,35,434,434,400,35,434,434,434,400,35,434,434,434,434,400,35,434,434,434,434,434 for sample 002
On chr3:195506451 (ref:AGGGGTGGCGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGG; alt:A), I found 0/1:0,54:54:99:4354,0,309 for sample 003
This kind of problem happens to both SNV and Indels. Is this a result of a bug, or is there anything I missed? I can provide more information if needed. Thanks a lot!