Hi Sendu,
with --no-BAQ, any existing BAQ information is ignored.
Thanks for the usage text, it is fixed now.
Best wishes,
Petr
On Mon, 2018-09-24 at 11:14 +0100, Sendu Bala wrote:
> 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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