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Search: Posts Made By: asebastian
Forum: Bioinformatics 04-06-2013, 01:56 PM
Replies: 0
Views: 1,243
Posted By asebastian
variant position - mpileup

Hi all,

I want to find the mean position of variant within reads. I am using samtools mpileup|bcftools for variant call.

Does anyone know how to accomplish this.

Note: I saw this question...
Forum: Bioinformatics 04-02-2013, 12:57 PM
Replies: 2
Views: 1,464
Posted By asebastian
Thanks David, With BioPerl, I am trying to...

Thanks David,
With BioPerl, I am trying to contact them...
As for the system calls, I am trying to avoid direct system commands... Thats why I was looking for a BioPerl wrapper...

-A
Forum: Bioinformatics 04-01-2013, 12:07 PM
Replies: 2
Views: 1,464
Posted By asebastian
BioPerl & Variant calling

Hi ,

I am trying to do variant calling with mpileup using BioPerl.
I am using Bio::Tools::Run::Samtools but it says mpileup not registered.
Does this mean BioPerl doesn't support mpileup ?
Can...
Forum: Bioinformatics 03-31-2013, 08:53 PM
Replies: 0
Views: 1,552
Posted By asebastian
Variant Calling with mpileup

Hi all,

I am a new bee to variant calling. I am using samtools mpileup. My criteria includes:
-- minimum total coverage of 5
-- minimum variant-supporting coverage of 2
-- minimum average base...
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