Question: Bed File Coordinates
0
gravatar for win
8.2 years ago by
win860
India
win860 wrote:

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

bed tabix • 2.7k views
ADD COMMENTlink modified 8.2 years ago by Zev.Kronenberg11k • written 8.2 years ago by win860

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

ADD REPLYlink written 8.2 years ago by Sukhdeep Singh10k
0
gravatar for Zev.Kronenberg
8.2 years ago by
United States
Zev.Kronenberg11k wrote:

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

ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Zev.Kronenberg11k
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