[Bioperl-l] 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 asma.rabe at gmail.com" <bioperl-l-bounces+cjfields=illinois.edu at mailman.open-bio.org on behalf of asma.rabe at gmail.com> 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
>
>
>
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