Apologies if this is mentioned in the documentation, I wasn’t able to find it.
Are the start coordinates of variants in VDS format considered 0-based (like BED), or 1-based (like VCF)?
Thank you.
We don’t change them when importing from VCF.
To give a better answer, I think you can assume that start coordinates are 1-based, since in KeyTable.import_bed, we add one to the start.
Ok, good to know. Thanks!
I found this in the documentation, it confirms starts are 1-based:
Attributes
alt_alleles List of alternate allele objects in this polymorphism.
contig Chromosome identifier.
ref Reference allele at this locus.
start Chromosomal position (1-based).
aha! glad it’s there somewhere, even if it’s not easy to find!