Fix dash/empty ALT alleles for deletions in VCF
I have a VCF file that has deletions specified like this, with the REF allele containing only the deleted portion and the ALT allele just saying -:
chr1 101 . AAA -
I would like to combine this with another VCF in which deletions are specified like this, with REF and ALT both extended by 1bp to the left to ensure neither is empty:
chr1 100 . GAAA G
Is there a tool to convert from one of these representations to the other? I have already tried vt normalize and bcftools norm but neither of them seem to do this.
I don't really mind which representation I end up with although I think the second is the one more consistent with the spec.
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These are different VCF formats - the first is quite old (3.x). There could be something to convert v3.x to v4+, but a preliminary search does not yield any obvious results.
Hello bbio!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/q/9229/650
This is typically not recommended as it runs the risk of annoying people in both communities.