bcftools mpileup has options --no-BAQ ("disable BAQ") and --redo-BAQ
("recalculate BAQ on the fly, ignore existing BQs").
What is the default behaviour given a bam with BAQ tags?
Does --no-BAQ turn off all consideration of BAQ, or turn off its own
calculation of BAQ (considering existing BAQ tags if present)?
Cheers,
Sendu.
PS. The help text for `bcftools call` suggests using "in conjunction with
samtools mpileup". Should that be "in conjunction with bcftools mpileup"
instead?
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