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.
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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 -
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?
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