Entering edit mode
4.3 years ago
dec986
▴
370
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?
It looks like the tool uses
end = start + 1
instead ofend = start + length(ref) -1
. You could either useawk
to solve this yourself or submit a bug-report to vcf2bed (assuming this feature is not already implemented).