finding copy number variation from bam file.

Question

[Varun Gupta]

Hi Everyone

I am interested in finding CNV's for my sample. I aligned the reads with ref genome using bwa mem and obtained bam file. I looked at Varscan for CNV's but it requires 2 bam files ; normal/ref and sample. Is there a tool which can find CNV's on only single bam file? My reference genome is yeast

Hope to hear from you

Regards
Varun

[Adrian Pelin]

All tools are based on coverage or sequencing depth. Why don't you calculate the average coverage of the ref genome and then find regions that are double or triple in coverage. This may not be the appropriate way to do it, but it should agree somewhat to what other tools are suggesting.

[Varun Gupta]

Hi Adrian,

I have a single sample which was UV radiated and I mapped it to yeast ref genome. How can I get average coverage of the ref genome. From the bam file of the sample I can get the coverage of the sample, but how for reference?

Thanks

[Adrian Pelin]

Download an SRA that sequenced a wt yeast?

Answer 1

[Ashutosh Pandey]

CnD works great for inbred organisms like mouse, yeast.

Other tools:

• CNV tools
• CNVnator