cannot join group

[Nicholas Beckloff]

Dear BEDtools group,
  For some odd reason I cannot join this group despite having a gmail account. I also cannnot post my question, which is how to make a SNP file using BEDtools. Can anyone assist me in this endeavor?

Thanks,

--
S Honcho

[Aaron Quinlan]

Hi S Honcho,

Because the start position in BED files is 0-based, one must create SNP files as follows (fictitious SNPs):

chr1 0 1 snp_at_1st_base_on_chrom1

chr3 999999 1000000 snp_at_1millionth_base_on_chrom3

BEDTools does not create SNP files per se.  This must be done with external programs (e.g. samtools, gigaBayes, MAQ, etc.).  BEDTools can then compare SNP files (in the above format) to other annotation files in BED format.

Aaron