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zjshi / Maast

Microbial agile accurate SNP Typer
MIT License
29 stars 2 forks source link

VCF file format #15

Closed snayfach closed 2 years ago

snayfach commented 2 years ago

Are we sure that the current format is correct? Do you know anyone who uses VCF files? Maybe they could test it out to make sure it works with standard programs.

One easy fix is to update the source field:

source=https://github.com/snayfach/snpMLST

I'm not sure what the differences are, but there's not a 4.2 version of the format: https://samtools.github.io/hts-specs/VCFv4.2.pdf

It's not clear what nucleotides the 4 genotypes refer to:

GP1:GP2:GP3:GP4

zjshi commented 2 years ago

Applied the easy fix as well as improved GP1:GP2:GP3:GP4 description.