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Converting a VCF with SNPs and indels to BED format

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  • Converting a VCF with SNPs and indels to BED format

    Does anyone know of tools or have custom scripts (aside from "vcf2bed") that are able to convert between a VCF containing both indels and SNPs into BED format? The tricky part is creating the correct BED regions to capture the indel variants, and I haven't been able to find anything on the internet thus far.

  • #2
    This should do the trick right?

    Code:
    awk '! /\#/' Variants.vcf | awk '{if(length($4) > length($5)) print $1"\t"($2-1)"\t"($2+length($4)-1); else print $1"\t"($2-1)"\t"($2+length($5)-1)}' > Variants.bed

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    • #3
      Does anyone know how to incorporate the reference/variant nucleotides into this script? I'm specifically hoping to achieve the following format from a .vcf input file:

      CHR \t 0-POSITION \t 1-POSITION \t REF|ALT

      e.g.

      chr02 1242 1243 A|G

      Alternatively if there are software packages that can be used to do this, what's the best option?

      Thanks

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