Samtools: SNP calling from only coding regions

[newbietonextgen]

Hi all ,

I was wondering if i could use samtools to just pull out the SNP from the coding regions? I have SNP from the genome/single chr. I think i saw a code sometime back but could be mistaken. It will be great is some one could point me to one...

Thanks

[vgrubor]

Hi all ,

I was wondering if i could use samtools to just pull out the SNP from the coding regions? I have SNP from the genome/single chr. I think i saw a code sometime back but could be mistaken. It will be great is some one could point me to one...

Thanks

What you need:
SAMtools
awk
BEDTools
bed file containing coordinates of exons (CCDS recommended for human genome)

call SNPs with samtools and pipe the output to awk to generate a bed file and then pipe that to intersectBed to filter calls that fall within the exon coordinates.

[newbietonextgen]

Thanks for the reply. I just forgot about BEDTools. Since i am not working on the mouse or human model, does the UCSC gene browser has the coordinates of exons for other sequenced individuals?

[vgrubor]

All human individuals share the same exon set. CCDS is a curated set of exons. You should use it to look at differences between individuals.

[newbietonextgen]

Thanks for this suggestion but what if you are working on other models (other than human and mouse). Is there a online tool/resource (UCSC, Ensemble) for finding out just the coordinates for the exons? Pleasel let me know.

Thanks

[vgrubor]

Depends on the organism. UCSC is just one repository for genomic information. It contains information on the following species:
Human,Chimp, Orangutan,Rhesus,Marmoset, Mouse, Rat, Guinea pig, Rabbit, Cat,Panda, Dog, Horse, Pig, Cow, Elephant, Opossum and Platypus

Drosophila has its own browser also. Some species are not model organism so they wouldn't have that much information available. I would try the following Google search: <your species name> genome browser. If anything exists it should show up.
Hope this helps.