avoid answering something unrelated to the question.
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.
2 answers
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)
Just remember no matter 0 based or 1 based, the later number will be the position for that base, such as chr1:1-2 and chr1:2:2
Another interesting thing is that if you read chrosome into memory with PERL, be careful, perl is 0 based in its array. Therefore, for example, the 5th base in perl array will be $read[4] and will be shown as chr1:4-5 and chr1:5-5 in UCSC.
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