I have just gotten my sequencing data, and I want to find snp:s in it. I have seen some examples on how to do it with bowtie as aligner and samtools mpileup for snp detection, but are there any other way that might be better than this approach?
Best regards Anna
asked 19 Oct '12, 12:03
You might want to checkout Broads best practice for variant detection using the GATK: http://www.broadinstitute.org/gatk/guide/topic?name=best-practices#best-practices1186
They suggest using BWA for alignment, but you should be able to use bowtie (or any other aligner capable of outputing bam-formated alignments) for alignment and still apply the rest of the workflow.
answered 19 Oct '12, 16:34
Not sure if better than samtools but you could use GATK to call snps. Here is an example GATK snp calling workflow from seqanswers
If someone else knows good comparisons between tools or other tools for snp calling please chime in :)
answered 19 Mar, 14:19
I realize that this answer may be about six months too late, but anyway...
Broad recently published a series of video lectures from their GATK workshop in December 2012, which goes into a lot of detail about the best practices pipeline. You should take a look if you still need to know more about SNP calling: http://www.broadinstitute.org/gatk/guide/events?id=2038
There is also suggestions for parameters to use when calling the variants: http://gatkforums.broadinstitute.org/discussion/1259/what-vqsr-training-sets-arguments-should-i-use-for-my-specific-project
The latter is more "hands-on" and may be more helpful if you want to get started quickly and do not care so much about the details. :)
answered 17 Apr, 15:30