creating specific bed file from VCF
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22 months ago
dec986 ▴ 300

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?

vcf vcf2bed • 289 views
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It looks like the tool uses end = start + 1 instead of end = start + length(ref) -1. You could either use awk to solve this yourself or submit a bug-report to vcf2bed (assuming this feature is not already implemented).

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