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Old 01-31-2014, 10:41 AM   #1
Location: New York City

Join Date: Mar 2013
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Default Strand orientation from VCF file


I am trying to figure out how I can get the strand orientation of each call made on a snp.vcf file. Does anyone know of a way?

In the end I am looking for this in one file complete file.
chr strt end ref alt strnd_orient(+/-) associated_gene

I have tried using this Bedtools command but was not successful
intersectBed -a Benign.vcf -b ucscRetro_hg19.bed -header -wao 1> test

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Old 01-31-2014, 11:34 AM   #2
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Location: Denmark

Join Date: Jul 2012
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I think all reported calls are assumed to be on the forward strand in VCF specification.
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