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.
-
-
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?
ThanksComment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment