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Consider removing the BAQ option in samtools mpileup #154

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mfoll opened this issue Mar 8, 2017 · 0 comments
Open

Consider removing the BAQ option in samtools mpileup #154

mfoll opened this issue Mar 8, 2017 · 0 comments
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mfoll commented Mar 8, 2017

Adding the --no-BAQ in samtools mpileup causes:

Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.

Disabling the BAQ makes it roughly 33% faster, so we should evaluate if this is necessary in the case of needlestack (in particular when we do ABRA).
@mfoll mfoll self-assigned this Mar 8, 2017
@tdelhomme tdelhomme added this to the v2.0 milestone May 18, 2018
@mfoll mfoll removed this from the v2.0 milestone Jun 12, 2020
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