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Realign all reads at target site, not just reads with no mismatches #1469

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fnothaft opened this issue Apr 3, 2017 · 0 comments
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Realign all reads at target site, not just reads with no mismatches #1469

fnothaft opened this issue Apr 3, 2017 · 0 comments
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enhancement
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0.22.0

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fnothaft commented Apr 3, 2017

Currently, we skip reads that do not have mismatches. It turns out that this doesn't save much time, and leads to a slight accuracy cost on homozygous alt INDEL calls.
@fnothaft fnothaft added this to the 0.22.0 milestone Apr 3, 2017
@fnothaft fnothaft self-assigned this Apr 3, 2017
fnothaft added a commit to fnothaft/adam that referenced this issue Apr 3, 2017
@fnothaft
[ADAM-1469] Don't filter on whether reads have mismatches during real…
3670c7e 
…ignment

Resolves bigdatagenomics#1469. Provides approximately a 1% bump in both INDEL calling precision
and recall.
@fnothaft fnothaft mentioned this issue Apr 3, 2017
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heuermh pushed a commit that referenced this issue Apr 3, 2017
@fnothaft @heuermh
[ADAM-1469] Don't filter on whether reads have mismatches during real…
8df3aa2 
…ignment

Resolves #1469. Provides approximately a 1% bump in both INDEL calling precision
and recall.
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