Confused by overlapping indels
Hi all, I'm currently confused about the snips called as shown below. If I am not mistaken, the first row shows gatk called an 34 bp insertion in sample 001 at position 3229753. It didn't call anything for sample 001 on position 3229753, but then for position 3229756, it calls another 15bp insertion for sample 001, which overlaps completely with the first insertion.
I have three questions about this.
1) Is my interpretation of the data shown below correct
2) If this is correct, is this expected behaviour for gatk? What kind of circumstances are expected to generate these results?
3) How can I interpret these conflicting snips, should I just pick the call with the highest confidence and ignore the other? What about if a lower-confidence call is a substring of a previous call in another sample?
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 001 002 003 004 gi|ref| 3229753 0 A AACTTGCCTGCCACGCTTTTCTTTATACTTAACCC 9635.2 0 AC=3;AF=1.00;AN=3;DP=304;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=59.86;QD=29.65;SOR=0.779 GT:AD:DP:GQ:PL 1:0,48:48:99:2153,0 1:0,84:84:99:3696,0 .:0,0 1:0,85:85:99:3813,0 gi|ref| 3229754 0 A ACTTGCCTGCCACGCTTTTCTTTATACTTAACCCAGGCGCTAATTCATCTGCAACG 3012.2 0 AC=1;AF=1.00;AN=1;DP=291;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.91;QD=28.35;SOR=0.910 GT:AD:DP:GQ:PL .:0,0 .:0,0 1:0,69:69:99:3039,0 .:0,0 gi|ref| 3229756 0 G GCGCTAATTCATCTGC 3654.2 0 AC=3;AF=1.00;AN=3;DP=74;FS=0.000;MLEAC=3;MLEAF=1.00;MQ=60.00;QD=28.36;SOR=0.747 GT:AD:DP:GQ:PL 1:0,17:17:99:854,0 1:0,25:25:99:1213,0 .:0,0 1:0,32:32:99:1614,0