Test-drive the GATK tools and Best Practices pipelines on Terra
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I found in called variants from HaplotypeCaller function a false positive.
The program detect this insertion:
chr2 179301046 . T TTAAAGAAATGTGGTTCTCTGGAGAAATATTACTAAATTTGG 653.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.246;ClippingRankSum=-0.687;DP=94;FS=90.056;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.377;QD=6.95;ReadPosRankSum=-1.726 GT:AD:DP:GQ:PL 0/1:46,24:70:99:691,0,12364
but it does not exist (see attached image). In the CIGAR of the reads the insertion is not indicated.
Interestingly, UnifiedGenotyper does not call the variant.
Anyone has some idea about this error and how fix it?
Thanks a lot