Bed File Coordinates

Question

[win]

Hi all, In a spreadsheet i have my list of rs# with their chromosomal number and locations. I want to generate a BED file for these variants. I wanted to know if the start and end coordinates should be the same or should they be offset by 1.

For e.g. Chr1:1000,1000 or Chr1:1000,1001 or Chr1:999,1000

where 1000 is the chromosomal coordinate for that rs#.

the BED file will be used as an input region file to query a VCF file using tabix.

thanks in advance. a

[Sukhi Singh]

Sorry, could you please say what rs# means, google didn't helped me as well :)

Answer 1

[Zev.Kronenberg]

Directly from Tabix.

-e INT   Column of end chromosomal position. The end column can be the same as the start column. [5]

So yes: Start = Stop