Missing RUNX1 insertion in 7075-04-001-002
7075-04-001-002: RUNX1 c.1342_1354dupAACCAGAGCGACG.
The mutation shown above is not found with the latest version of HAMLET. The insertion has been validated using PCR+Sanger sequencing, so we are certain this insertion is valid.
After investigation, the issue has been narrowed down to the GSNAP aligner, which in the latest version of HAMLET still maps the reads to RUNX1, but does not detect the insertion.
gmap version | CIGAR of mapped read | Indel found | Comment |
---|---|---|---|
gmap-2014-12-23 | 28M98N1D48M13I62M | Yes | |
gmap-2015-12-31 | 28M99N48M13I62M | No | Only a few reads have the insertion |
gmap.2019.06.10 | 28S55M68S | No |
The previous version of gmap, which did identify this insertion, was gmap-2014-12-23
, which was custom compiled for the shark cluster.
The updated version of HAMLET has version gmap:2019.06.10
, which is much more recent, but appears to be less likely to call insertions.