Question: Copy number variation detection
gravatar for v27
20 months ago by
v2710 wrote:

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)

sequence next-gen genome • 623 views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 20 months ago by v2710

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.

ADD REPLYlink written 20 months ago by ATpoint28k
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