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Realign or sanity check assembly anchor #113

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d-cameron opened this issue Feb 22, 2018 · 0 comments
Closed

Realign or sanity check assembly anchor #113

d-cameron opened this issue Feb 22, 2018 · 0 comments
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bug enhancement

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d-cameron commented Feb 22, 2018 •
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Misassembly can result in the assembly anchor sequence being offset from the actual position. This results in the variant position offset by the error size. The call position for these rare cases can be corrected by one of :

  1. SmithWatermann realignment of assembly anchors
  2. External realignment of entire assembly contig
  3. Filtering of assemblies based on NM.

(2) is probably the best option as it also reduces the false positive rate as multi-mapping contig are unlikely to make back to their original alignment location.
d-cameron added a commit that referenced this issue Apr 3, 2018
@d-cameron
#113 realigning assemblies and only including them when the realignme…
9ef8ee0 
…nt overlaps the originating assembly position

Added SoftClipsToSplitReads REALIGN_ENTIRE_READ to implement #113
Added FIX_DUPLICATE_FLAG to correct incorrect duplicate marking of split reads.
Not filtering duplicate reads in CallVariants ExtractSVReads so FIX_DUPLICATE_FLAG actually works
Added SoftClipsToSplitReads REALIGN_EXISTING_SPLIT_READS and softclip.realignSplitReads configuration setting
Added external aligner support for windows using WSL
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