0-based VCF output

[hdashnow]

Hi! I noticed that atarva accepts a 0-based bed regions file as input and also produces a 0-based VCF as output. VCF format should be 1-based (see below). This creates off-by-1 errors in our downstream analyses.

A nice summary of this common problem:
https://www.biostars.org/p/84686/

The VCF spec:

POS- position: The reference position, with the 1st base having position 1. Positions are sorted numerically, in increasing order, within each reference sequence CHROM. It is permitted to have multiple records with the same POS. Telomeres are indicated by using positions 0 or N+1, where N is the length of the corresponding chromosome or contig. (Integer, Required)

May I suggest that you produce 1-based VCFs?

Warm regards,
Harriet

[Dhaksnamoorthy]

Hi @hdashnow,
Thank you for raising this issue and for providing the references. This issue has already been resolved in the dev branch (see #7), and we have now merged the fix into the master branch with the release version v0.5.0.

Please let us know if this works as expected and resolves the issues in downstream analyses.