creating specific bed file from VCF
I'm attempting to create a region file for break_blocks, which has a very specific format requirement
for example:
1 1272857 1272858 ZYX-rs77443780 . C T
1 1273477 1273478 seq-rs797044834 . GGGGGCAGCCGGGT G
but this issue is that I don't think that the last end 1273478 is correct. This represents a large deletion, so this should be 14 characters shorter (or longer?) this output is from vcf2bed
is there a vcf2bed like tool that can do this? or do I need to write a script to do this?
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It looks like the tool uses
end = start + 1instead ofend = start + length(ref) -1. You could either useawkto solve this yourself or submit a bug-report to vcf2bed (assuming this feature is not already implemented).