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Forum: Bioinformatics 10-21-2014, 03:57 AM
Replies: 0
Views: 2,160
Posted By JadeB
Filtering VCF file

Hi,

I'm currently trying to filter my VCF file. I'm working on mtDNA, so I'd like to exclude heterozygous SNP. To do so, I'v tried to use bcftools filter and bcftools query, but I don't manage to...
Forum: Bioinformatics 10-17-2014, 03:20 AM
Replies: 8
Views: 2,365
Posted By JadeB
No, my sam files are gsnap output, not made with...

No, my sam files are gsnap output, not made with samtools view, then I'm trying to have bam files...

I'm currently trying an other thing : error could maybe be linked with different names between...
Forum: Bioinformatics 10-17-2014, 02:23 AM
Replies: 8
Views: 2,365
Posted By JadeB
I'm actually using the 0.1.19-44428cd one. ...

I'm actually using the 0.1.19-44428cd one.

But, I don't have something like "missing EOF marker", only lines as above (for files which are not empty), and "Your job has been killed."

I have bam...
Forum: Bioinformatics 10-17-2014, 02:09 AM
Replies: 8
Views: 2,365
Posted By JadeB
Ok. Thanks a lot for your answers. If I...

Ok. Thanks a lot for your answers.

If I don't need it, it's ok. But I thought my next error message was due to this lack.

In fact, when I do this :



or this :
Forum: Bioinformatics 10-17-2014, 01:43 AM
Replies: 8
Views: 2,365
Posted By JadeB
GSNAP and SAM header

Dear all,

I'm currently trying to align reads on a reference sequence with gsnap with this code :



I'm working with very short reads, it's why i'm using the clip-overlap command.

Work is...
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