Trying to use OncoSNP-SEQ for CNV

[lethalfang]

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,

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.

[esraa]

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.

[esraa]

I have the same problem ?any suggestion