Hi all, 

I'm working with a vcf (v4.1) that has incorrectly formatted deletions for some reason. The insertions are fine, but the deletions are annotated as (example):

    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
    2	32474671	indel.60227	A	-	.	PASS	.	GT	

Notice that the ALT is `-`, when the line should have been formatted as such (example):

    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
    2	32474670	indel.60227	GA	G	.	PASS	.	GT	

I have no idea how the deletions ended up like this in the vcf, but my present plan is to parse a reference genome fasta file for these positions and manually correct all the deletion annotations, so I don't have to drop them from the vcf. What I wanted to know is if there's a tool that already does this- as it stands, I'm writing a manual parser. 
I wound up just parsing the vcf in Python and calling samtools to correct the deletions in the vcf. By subtracting 1 from the alleged bp_pos, calling `samtools faidx <reference_genome> chr:del_start-del_end` for each REF, and taking the first character of that for ALT, you can fill in the blanks. I don't believe there's a tool that corrects this problem in VCFs, because I don't think this is a common (or normal) problem. Leaving this here in case anyone ever encounters the same situation. 