Copy number variation detection

Question

[v27]

i want to detect copy number variation among gene from whole genome sequencing data of bacteria. I have an idea how to detect the SNP/SNV's. i have the used sam/bam/vcf/bcf tools to detect it.

I have tried using the VarScan ...but i get an error.

Could someone suggest a command line tool to detect the CNVs from WGS using NGS (please give reference of a paper)

[ATpoint]

Hi v27,

before dealing with the question, I may suggest to read this post on how to ask a good question in order to motivate people to invest time in an elaborate answer.

Towards the CNVs, this post suggests a few tools, including VarScan. To work out why VarScan fails in your case, please give the full command line and the error message.