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Assembly support contribution for spanning assemblies is not recalculated for each span. #114

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d-cameron opened this issue Feb 27, 2018 · 0 comments
Closed

Assembly support contribution for spanning assemblies is not recalculated for each span. #114

d-cameron opened this issue Feb 27, 2018 · 0 comments
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bug enhancement

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@d-cameron
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A germline indel 50bp away from a somatic variant will cause the somatic variant to have conscripted assembly support since.

The breakdown of assembly support should be recalculated for each span (per bp is probably the easiest implementation) and only reads actually supporting that breakpoint should be considered supporting.
d-cameron added a commit that referenced this issue Apr 5, 2018
@d-cameron
#114 Added category support CIGAR to assembly output
6545e13
d-cameron added a commit that referenced this issue Apr 5, 2018
@d-cameron
#114 categories that contribute to the assembly but not the breakpoin…
aaf7e3f 
…t are excluded from the assembly breakpoint scoring

This is configurable by the variantcalling.requireAssemblyCategorySupport property
d-cameron added a commit that referenced this issue Apr 5, 2018
@d-cameron
#114 including read pair anchors when calculating per category support
ede0227
d-cameron added a commit that referenced this issue May 21, 2018
@d-cameron
Updated VF and BCF to incorporate #114
6343413
d-cameron added a commit that referenced this issue May 21, 2018
@d-cameron
Updated VF and BCF to incorporate #114
4505f08
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