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GATK calling on del/ins at same location
I mapped using both BWA and novoalign.
In my sample on gene DHCR7 on chr11, there is Deletion and Insertion at same location. Del of 4 bases (GACG) at chr11: 71,155,132 - 71,155,135 AND insertion of 11 bp CGTCACCGGAC
After alignment in IGV, it shows up as insertion of CGTCACCG between 71,155,131 and 71,155,132 and deletion of bp 71,155,135 (G) . It ends up being called as separate variant which is wrong
IGV is attached. Any inputs of correcting is appreciated. How does GATK algorithm handles this - how about local realignment by haplotyper ?