Recurrent artifact in SOPHIA (v35) workflow 2.2.3_v1_0

[naveedishaque]

Dear SOPHIA workflow team,

I have found that the SOPHIA workflow v2.2.3_v1_0. I have seen this pop up in Heidelberg HIPO projects and now also in some Berlin projects. My student (@niklasmueboe) looked into this and found that:

• The recurrent artifact SV is 5 155401529 155401530 5 155401583 155401584
• Niklas validated that this is a small-ish deletion via IGV using the visualise.py tool
• This position has no reports in the MREF with 3417 control samples
• I have seen this position as a false positive in numerous HIPO projects, but others might have missed it as the Sophia workflow uses the "wrong" gencode annotation (v27 vs v19 as all other workflows), and this gene reference does not annotate a gene in this region, but gencode 19 does (SGCD)

What is the best way to correct this? Updating the MREF, or post-filtering in the workflow, or updating the downstream script to filter?

:D