On Mon, Oct 02, 2017 at 01:05:03PM +0800, ?? wrote:
> I first check 20763685 position, it has 491 reads, and one read is at its
> end. Then I check 20763686 position, but only got 172 reads. Where are the
> 318 reads that should appear? Anyone has any idea why this happens?
What happens if you add -B to your mpileup command? This disables the
BAQ algorithm.
It can sometimes do strange things and I don't entirely understand
what it's doing! Overall it's a force for good, hence enabled by
default, but I've seen several places where it introduces errors too.
Naively I'd expect 20763686 to be the same regardless of
whether we started at that coordinate or not. Is this the case? If
you supply a region 20763685-20763686 do you get the same drop for
20763686 that you see with 20763686-20763686? If so, then it's some
per-location filtering method that is stripping the bases at that
specific site (with BAQ being the usual suspect). If not then it's
probably a bug.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
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The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
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