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Old 09-21-2010, 01:25 PM   #1
sukhbat
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Location: Utah

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Default SOAPsnp pileup viewer

I'm using SOAPsnp to identify SNP. Is there any visualization for SOAPsnp pileup?
Thanks, guys.
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Old 09-21-2010, 01:42 PM   #2
svl
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Quote:
Originally Posted by sukhbat View Post
Is there any visualization for SOAPsnp pileup?
What exactly do you want to visualize? If think you want to see the mapped reads and where they differ from reference (known/possible SNPs) as stacked output (so all complete reads!)... If so you should use mapping output to visualize that. For example SAM/BAM format in IGV, you will see all mapped reads stacked on top of the reference sequence. See links:

For SOAP I see there is a soap2sam converter (perl script):
http://soap.genomics.org.cn/

In IGV you can load and view SAM/BAM:
http://www.broadinstitute.org/igv/

Or try some other NGS viewer, for a software comparison:
http://lh3lh3.users.sourceforge.net/NGSalnview.shtml
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Old 09-23-2010, 01:05 PM   #3
sukhbat
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Thanks man!
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