On Wed, Jul 12, 2017 at 04:41:17PM +0200, Kristian Ullrich wrote:
> whatever I am doing with both 'samtools mpileup' and 'bcftools
> mpileup', in both cases not all sites are reported, even if I
> specify the '-a -a' options e.g.:
My standard first try at explaining anything odd with mpileup is to
test it with (default) and without (-B) the BAQ calculation. Also
consider -A too.
Does adding -B change things for you? (If it does, explaining why and
deciding if it is an improvement is a totally different and more
complex issue!)
James
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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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