Question: finding copy number variation from bam file.
0
gravatar for Varun Gupta
4.4 years ago by
Varun Gupta1.1k
United States
Varun Gupta1.1k wrote:

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

cnv • 3.6k views
ADD COMMENTlink modified 4.4 years ago by Ashutosh Pandey11k • written 4.4 years ago by Varun Gupta1.1k

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.

ADD REPLYlink written 4.4 years ago by Adrian Pelin2.2k

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

ADD REPLYlink written 4.4 years ago by Varun Gupta1.1k

Download an SRA that sequenced a wt yeast?

ADD REPLYlink written 4.4 years ago by Adrian Pelin2.2k
1
gravatar for Ashutosh Pandey
4.4 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

CnD (https://www.sanger.ac.uk/resources/software/cnd/) works great  for inbred organisms like mouse, yeast.

Other tools: 

CNV tools (http://cnv-tools.sourceforge.net/CNVtools.html)

CNVnator (http://sv.gersteinlab.org/cnvnator/)

ADD COMMENTlink written 4.4 years ago by Ashutosh Pandey11k
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