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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Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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
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local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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http://lists.bx.psu.edu/
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