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Old 08-16-2012, 10:11 AM   #1
mathew
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Default coomercial or open source tool for CNV from sequence data

I was wondering if some one can point me to a commercial or open source tool to call SNPs as well Copy number variation from Illumina's sequencing data. Thanks.
Mathew
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Old 08-17-2012, 02:16 AM   #2
SES
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You might want to start by looking at the software page. Also, you might get more responses if you can refine your question.
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Old 08-17-2012, 02:31 AM   #3
Jane M
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Hi,
You can try VarScan, it's a free software, which gives SNP, indel and CNV.
Good luck,
Jane
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Old 08-21-2012, 02:19 AM   #4
brianp22
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The GenomeStudio Software package comprises seven discrete application modules that enable you to conveniently compare data from different applications.
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Old 08-24-2012, 06:44 AM   #5
shyam_la
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Quote:
Originally Posted by Jane M View Post
Hi,
You can try VarScan, it's a free software, which gives SNP, indel and CNV.
Good luck,
Jane
I have a related question: Can the copy number algorithm of VarScan still be used if my tumor and normal data are sequenced to varying depths? Lets says mean tumor depth is 2.5 times mean normal depth.. Is it still useful? If so, how should I modify the command line?
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Old 08-26-2012, 11:15 AM   #6
swNGS
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You might be better off with specific tools for certain aspects of he jobs hat you areatte,ping to do rather than looking for a 'one tool for all jobs, approach, which as far as I'm concerned doesn't really exist!
For variant calling I would suggest looking at the Broad's V3 exome pipeline and working from there. In addition to the CNV suggestions from above, have a look at CONTRA
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