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  • Strand orientation from VCF file

    Hello,

    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


    Thanks,
    Nino

  • #2
    I think all reported calls are assumed to be on the forward strand in VCF specification.

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