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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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 the enhancement label Apr 3, 2017

@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

[ADAM-1469] Don't filter on whether reads have mismatches during real…
…ignment


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

@heuermh heuermh closed this in #1470 Apr 3, 2017

heuermh added a commit that referenced this issue Apr 3, 2017

[ADAM-1469] Don't filter on whether reads have mismatches during real…
…ignment


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