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Forum: Bioinformatics 10-10-2012, 03:12 AM
Replies: 12
Views: 4,831
Posted By AWeller
You tell bcftools to only give you variants,...

You tell bcftools to only give you variants, maybe something is wrong with the snp calling, e.g. your quality is so low that it doesn't call any snps or there just are no snps?
Does samtools produce...
Forum: Bioinformatics 10-09-2012, 01:23 PM
Replies: 12
Views: 4,831
Posted By AWeller
The output you get is just the usual report...

The output you get is just the usual report samtools gives while running, not an error message.

Nobody will be able to answer your question with this little information, sorry.
Which command did...
Forum: Bioinformatics 09-06-2012, 01:46 AM
Replies: 2
Views: 1,522
Posted By AWeller
I'm not sure if I understand your question...

I'm not sure if I understand your question correctly.

In general, omitting the "-v" in bcftools will show you all positions, not just the variants.

A convenient way to manually inspect a...
Forum: Bioinformatics 06-02-2012, 09:55 AM
Replies: 2
Views: 1,315
Posted By AWeller
Hi Matina, i don't have personal experience...

Hi Matina,

i don't have personal experience with this function of pybedtools, but let me make a first guess until better answers will (hopefully) come:

the error message looks to me like python...
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