Creating SNP files in BED

[Nicholas Beckloff]

Can someone please tell me if its possible to create files to look at SNPs using BEDTools?

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Nicholas Beckloff

[Aaron Quinlan]

See this thread:
http://groups.google.com/group/bedtools-discuss/browse_thread/thread/a384416fbdbb1f7d

[Aaron Quinlan]

Hi Nick,

   I note the use of the phrase "look at SNPs".  If you are asking about how to visualize called SNPs from a next-gen experiment, I suggest that you use IGV (http://www.broadinstitute.org/igv) from the Broad Institute or Gambit (http://code.google.com/p/gambit-viewer/).  Each allow one to upload tracks in BED format (e.g., your called SNPs from samtools or Bowtie) along with the aligned sequences in BAM format.

Is this what you meant?  BEDTools could be used to complement this by allowing you to screen for SNPs that overlap other interesting features.  You could then create a new BED file based on these overlaps, upload it to the aforementioned viewers and refine your analyses.  

 

Aaron

Aaron Quinlan, Ph.D.
NRSA Postdoctoral Fellow
Hall Laboratory

University of Virginia

Biochem. & Mol. Genetics

aaronq...@gmail.com