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gymrek-lab / LongTR

Tandem repeat genotyping with long reads
GNU General Public License v2.0
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TR region BED file - are start coordinates 1-based or 0-based? #5

Closed bw2 closed 5 months ago

bw2 commented 5 months ago

Would be nice to clarify this @ https://github.com/gymrek-lab/LongTR?tab=readme-ov-file#tr-region-bed-file

2. The start position of the TR on its chromosome
heliziii commented 5 months ago

Hi Ben,

Start coordinates should be 1-based. I will add this to the documentation. Thank you!

Best, Helia

davidlougheed commented 3 months ago

Hello, It's worth noting that the UCSC and GA4GH BED specifications both require 0-based, half-open coordinates: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 ; https://github.com/samtools/hts-specs/blob/master/BEDv1.pdf