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-tp40... 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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