Get strand from pos

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Get strand from pos

asma.rabe

Hi all,

I have variant list and I would like to get the sequence and strand for each position. I could get sequence using Bio::DB::Fasta
But I am not sure how to get strand information using position only ??

Any help is appreciated



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Re: Get strand from pos

Fields, Christopher J
Variant calls are made using a haploid reference genome for comparison and context (‘+’ strand, from 5’ to 3’), so strand is normally not reported as everything is based on the ‘+’ strand.  Offhand I don’t recall any VCF reports where strand is reported, and I’m struggling to think of a reason where this would be necessary.  Maybe epigenmoic modifications on one strand (is that even reported in VCF)?

chris


On 11/11/15, 10:58 AM, "Bioperl-l on behalf of [hidden email]" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:

>
>Hi all,
>
>I have variant list and I would like to get the sequence and strand for each position. I could get sequence using Bio::DB::Fasta
>But I am not sure how to get strand information using position only ??
>
>Any help is appreciated
>
>
>
>_______________________________________________
>Bioperl-l mailing list
>[hidden email]
>http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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