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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: