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Old 03-11-2014, 03:35 PM   #1
lethalfang
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Location: San Francisco, CA

Join Date: Aug 2011
Posts: 91
Question Trying to use OncoSNP-SEQ for CNV

Hi guys,

Does anyone have experience using OncoSNP-SEQ?

It's a somatic copy number alteration detector, geared toward tumor-normal paired whole genome sequencing data. It uses read counts and B allele frequencies, as well as mappability correction, GC content correction, etc.

But I have trouble get it going.
https://sites.google.com/site/oncosnpseq/usage

When I tried this,

Code:
perl process_pileup.pl --infile {NAME OF PILEUP FILE} --outfile {NAME OF ONCOSNP-SEQ FORMAT FILE} --snpfile {NAME OF BED FORMAT SNP FILE}
My outfiles are all empty (except for the header).

Thanks in advance.
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Old 03-09-2016, 10:31 AM   #2
esraa
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I try to run this code but I have error when mex viterbi_liteC.c file , also is samtool pileup work with windows or just C.
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Old 05-09-2016, 12:36 PM   #3
esraa
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I have the same problem ?any suggestion
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cna, cnv, copy number analysis, oncosnp-seq

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