Question: Is Position In Vcf File 1-Based (First Index Is At 1 Not 0)?
2
gravatar for jessada
8.3 years ago by
jessada130
jessada130 wrote:

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.

vcf • 8.8k views
ADD COMMENTlink modified 24 months ago by Shicheng Guo8.3k • written 8.3 years ago by jessada130
5
gravatar for Pierre Lindenbaum
8.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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)

ADD COMMENTlink modified 9 months ago by RamRS27k • written 8.3 years ago by Pierre Lindenbaum129k
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