Missing TET2 insertion in 7075-04-001-005
Due to a single bp insertion in TET2 that is not detected, 3 SNPs are erroneously called in validation sample 7075-04-001-005.
chr4 105259626 . T TG .
The first view in IGV is with the old version of gmap (gmap-2014-12-23), which does detect the insertion.
The site of the insertion is 8bp away from an intron boundary, which appears to be involved in this issue. There are a few reads that overlap the intron, and here the insertion is detected by the recent version of gmap(2019.06.10--pl526h2f06484_0)