Hi Yan,

I know that you have already start this analysis with one method, as posted here:
http://gmod.827538.n3.nabble.com/How-to-extract-geneID-from-pileup-file-tp4036039.html

But I wanted to follow-up and let you know that there are actually many ways to go about doing this in Galaxy. Which is best can subjective, although when working with DNA - use tools for DNA, when you have RNA - use tools for RNA (in particular mapping tools!).

I'll group by step.


*Alignments*:

BWA and Bowtie2/Tophat2 are good choices. Bowtie/Tophat would be less desirable (do not call indels as well). Reading each tools documentation, or searching seqanswers for discussions on the subject will give anyone a good idea about why - but the final call is yours - use what works for you.

*Calling/Filtering Variants:*

Freebayes, Pileup/Mpileup, other tools in 'NGS: SAM Tools' that filter/convert pileup files Tools in 'NGS: Indel Analysis' - 'snpEff' - 'GATK (beta) - 'Genome Diversity' - 'NGS: Variant Detection'
*
**Annotating Variants:*

SNPEff, new Galaxy team's tools "Naive Variant Detector" and "Variant Annotator"
Many tools in the same tool groups above

Some of these tools are on Test https://test.g2.bx.psu.edu and/or require a cloud Galaxy instance because of intensive compute requirements http://wiki.galaxyproject.org/Cloud. Local or Slipstream are also options.

Hope this helps you and others thinking about this sort of analysis!

Jen
Galaxy team

On 8/22/13 6:37 PM, Yan He wrote:

Hi Jen and other Galaxy-users,

I am working on exome-capture sequencing with NGS. I am wondering if there is a tool to identify SNPs on Galaxy? I would like to get SNP information (position and allele frequency ) for each gene. Any information is highly appreciated! Thanks!

Best wishes,

Yan



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The Galaxy User list should be used for the discussion of
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