On Wed, Jul 12, 2017 at 05:54:06PM +0200, Kristian Ullrich wrote:
> HOWEVER, if I add the options '-u -v' so that the output should be
> uncompressed and in VCF format, than the output has duplicated
> POSITIONs and in total less than the expected 25000 sites, if I
> remove the duplicated. So there might be an issue in reporting the
> VCF output or in translating the compressed to uncompressed output.
It's unlikely to be a compression issue. Is this the latest samtools
and htslib release?
I don't see how specifying a single region could ever give duplicated
positions (and some missing) in VCF though, hence this is likely a
bug!
It is worth testing bcftools mpileup, just to be sure it's not been
fixed. The samtools mpileup -v code has migrated to bcftools now and
it's deprecated in samtools. There are some minor command line
differences and maybe other tweaks, so it's worth checking it there.
If it still fails with the latest bcftools code then can you please
file a ticket on github?
https://github.com/samtools/bcftools
Apologies for the problems.
James
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| 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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