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Issue created by van den Berg@rrvandenbergOwner

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.

VCF: 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 second view in IGV is with a more recent version of gmap (2019.06.10--pl526h2f06484_0), which erroneously calls 3 snps instead of the one insertion. image

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) image

Edited by van den Berg
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