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nested deletions found
I used GenomeAnalysisTK-2.7-4-g6f46d11 UnifiedGenotyper GLM=INDEL genotyper.ploidy = 1 and found the following 2 VCF entries:
supercont_1.11_pilon 517213 . ACAACAGCAACAG A 5990.97 . AC=1;AF=1.00;AN=1;DP=107;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=50.31;MQ0=0;QD=4.67;RPA=3,1;RU=CAACAG;STR GT:AD:DP:GQ:MLPSAC:MLPSAF:PL 1:0,69:102:99:1:1.00:6030,0
supercont_1.11_pilon 517222 . ACAG A 3486.97 . AC=1;AF=1.00;AN=1;DP=95;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=49.16;MQ0=0;QD=12.23 GT:AD:DP:GQ:MLPSAC:MLPSAF:PL 1:0,69:42:99:1:1.00:3526,0
Has anyone come across this kind of thing before? I'm under the impression the 2nd entry is redundant.
No recommendations to use a newer version please!