Opened 6 days ago

Closed 6 days ago

#1636 closed enhancement (fixed)

Structural variants are not classified correctly by SigProfiler which causes incorrect signatures

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: blocker Milestone: Reggie v5.5.2
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

It seems like the SigProfiler package has a bug in the sv_matrix_generator code. We are using the the breakpoints.bedpe file as input and SigProfiler uses the strand1 and strand2 columns to classify the variants (if the two locations are on the same chromosome). See the table below.

On the other hand, Viola-SV (see https://viola-sv.readthedocs.io/en/1.0.x-stable-doc/userguide/sv_position_specification.html) indicates a different mapping.

strand1 strand2 SigProfiler Viola-SV
+ - inversion deletion
- + inversion tandem-duplication
+ + deletion inversion
- - tandem-duplication inversion

Lyckily, SigProfiler also accepts a bedpe-like formation where the two strandX columns have been replaced with svclass. It should be relatively easy to implement the same classification as Viola-SV in our own code before sending it to SigProfiler.

Change History (1)

comment:1 by Nicklas Nordborg, 6 days ago

Resolution: fixed
Status: newclosed

In 8008:

Fixes #1636: Structural variants are not classified correctly by SigProfiler which causes incorrect signatures

Added the classification in the awk script that we already used to add an extra column ("sample") to the bedpe file.

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