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IARCbioinfo / needlestack

Multi-sample somatic variant caller
GNU General Public License v3.0
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Consider removing the BAQ option in samtools mpileup #154

Open mfoll opened 7 years ago

mfoll commented 7 years ago

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).