Is Position In Vcf File 1-Based (First Index Is At 1 Not 0)?

Question

[jessada]

I need to convert data parsed from UCSC genome browser into vcf format (for testing) but don't know about its exact position. I know that UCSC is 1-based but I'm not sure about vcf.

Answer 1

[Pierre Lindenbaum]

it's defined in the spec: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

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)