Copy number variation detection
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)
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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.