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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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