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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
Mathew
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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. -
Hi,
You can try VarScan, it's a free software, which gives SNP, indel and CNV.
Good luck,
JaneComment
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The GenomeStudio Software package comprises seven discrete application modules that enable you to conveniently compare data from different applications.Comment
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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?Originally posted by Jane M View PostComment
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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 CONTRAComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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