I've used CrossBow ( took 3 hours on a 3 node, 10 core Hadoop cluster ) and worked through the mouse, chromosome 17 example given in the manual successfully to the end.. I now have 276,819 SNPs in SoapSNP output format and all the intermediate files..
I want to view this stuff graphically - zooming in, exploding it, seeing if they cluster in certain areas etc - sort of like what the original paper http://genomebiology.com/2009/10/10/R112 does.
I think I'm looking for a graphical display tool - something that can take in the reference sequence of the mouse chromosome 17 (all 95 million bases of it), the SNP calls( all 276K of them ) that Crossbow produced in SoapSNP output format and then let me look at it visually.
A tool that could marry the two to produce a new sequence, substituting the SNPs at the relevant points would be nice too.
Is this asking too much ? I've seen some fancy graphical tools at the EBI and NCBI websites so they have to be there, surely? Any ideas ?
I want to view this stuff graphically - zooming in, exploding it, seeing if they cluster in certain areas etc - sort of like what the original paper http://genomebiology.com/2009/10/10/R112 does.
I think I'm looking for a graphical display tool - something that can take in the reference sequence of the mouse chromosome 17 (all 95 million bases of it), the SNP calls( all 276K of them ) that Crossbow produced in SoapSNP output format and then let me look at it visually.
A tool that could marry the two to produce a new sequence, substituting the SNPs at the relevant points would be nice too.
Is this asking too much ? I've seen some fancy graphical tools at the EBI and NCBI websites so they have to be there, surely? Any ideas ?
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