I want to identify CNV in tumor sample sequenced using exome sequencing. Most of the CNV tools support only with control sample. Kindly suggest me a tool for identifying CNV's for exome sequencing data without a control sample.
The BioConductor package exomeCopy does not require control samples. it uses a hidden Markov model approach to predicting CNVs.
http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html
and author's web page - http://mike-love.net/
P.S. found a public link to the publication as well:
http://cmb.molgen.mpg.de/publications/Love_2011_exomeCopy.pdf
Dear Malik Alawi,
I have already tried Control-FreeC. It doesn't support exome sequencing and target enrichment sequencing data.
Hi Malik Alawi,
Currently Im using Contrl-FREEC v6.8 . Even it gives error as,
"ERROR: Currently you need to provide a control sample ('mateFile' or 'mateCopyNumberFile') when you analyze targeted sequencing data to eliminate capture bias. The GC-content bias is not the only bias in targeted sequencing"
Even in the tutorial, the provided config file for exome sequening contains flag for control.
Hi Michael Black,
I tried ExomeCNV with different spec and sens, to understand the results. But I didn't understand what those values are and how to correlate those values to identify CNVs. I went through exomeCNV guidelines but there is no information about how to read the result file. I'm attaching the result file. Kindly help me out of this.
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