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Starting with a chromosome # and position, I am trying to get chromStart and chromEnd values for a .bed file, but I am not sure how to calculate chromEnd when I have a variant that is an insertion or deletion.

My file is not a VCF file but it gives the chromosome number, chromosomal position (pos), reference (ref) allele, and alternate (alt) allele for each genetic variant, like you would find in a VCF file. The tricky part is that not all of my variants are single nucleotide base changes--I also have insertions and deletions that can be multiple bases long.

For SNPs I am setting chromStart = pos - 1, and chromEnd = start + 1 = pos. (Note, .bed format requires 0-based indexing and the end position is exclusive. See https://genome.ucsc.edu/FAQ/FAQformat.html)

I am unsure of how to handle indels though (insertions and deletions). Currently I am adding the length of the reference allele to the starting position to get the end position (chromEnd = start + len(ref)). I am not sure if this is right though.

I will be using this .bed file with a .bed file from Gencode and bedtools. Does anyone know the standard way the research community (or at least Gencode) treats indels when determining chromosomal position for .bed files? Thanks!

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    $\begingroup$ Usually people don't convert such things to BED files. bedtools understands VCF format, so why not convert to that, since it seems most of the information is already there? $\endgroup$
    – Devon Ryan
    Oct 4 '17 at 6:53
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    $\begingroup$ Could you explain why you are trying to make this into a bed file? Is it for displaying it in a genome browser? I don't really see how a bed file could even show an indel, unless it were by using the coordinates of the reference genome. $\endgroup$
    – terdon
    Oct 4 '17 at 7:24
  • $\begingroup$ Hi, @terdon I am trying to make this into a BED file so that I can find which variants overlap exonic areas in the genome. I have a BED file from Gencode listing protein coding regions, and I want to know which of my variants overlap with the exome. $\endgroup$
    – Sarah
    Oct 4 '17 at 17:54
  • $\begingroup$ Hi @Devon Ryan, if the best thing to do would be to convert it to VCF format, will the bedtools intersect command be able to compare a VCF file with a BED file, or would I need to convert the Genecode BED to VCF? $\endgroup$
    – Sarah
    Oct 4 '17 at 17:55
  • $\begingroup$ bedtools is able to compare BED and VCF files, you don't need to convert anything at that point. $\endgroup$
    – Devon Ryan
    Oct 5 '17 at 6:57
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You can convert to VCF and use BEDOPS vcf2bed --insertions, vcf2bed --deletions and vcf2bed --snvs to segregate the VCF into three subsets.

For convenience, BEDOPS conversion tools deal with index shifts, including vcf2bed. The resulting BED file is 0-indexed, half-open.

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  • $\begingroup$ Thanks @Alex Reynolds. Is there any way to do this but without segregating the VCF into subsets? $\endgroup$
    – Sarah
    Oct 20 '17 at 1:29

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