Question: CNVkit- weird results when using the same sample as normal
0
gravatar for biobiu
27 days ago by
biobiu90
United States
biobiu90 wrote:

Hi, I'm using CNVkit to detect copy number alterations in hybridized capture panel. When I've used the same sample (exactly the same bam) as a reference I somehow do find some CNA. We used the batch command followed by the call command with default parameters (and with dropping low-coverage). 15 out of the 75 segments were found to have copy-number alteration (cn!=2). The cnn files are exactly the same both for the on- and off-targets so the problem starts when creating the cnr. Any idea why this discrepancy happens?

cnv • 104 views
ADD COMMENTlink modified 24 days ago by Eric T.2.4k • written 27 days ago by biobiu90
1
gravatar for Eric T.
24 days ago by
Eric T.2.4k
San Francisco, CA
Eric T.2.4k wrote:

Sorry, I'm not sure I follow. Could you paste both commands here so I can see the difference?

ADD COMMENTlink written 24 days ago by Eric T.2.4k

Thanks for your reply, I'll clarify. There are no two commands, just a batch command of the same sample as test and normal sample:

cnvkit.py batch SAMPLE.bam -n SAMPLE.bam --targets TAR.bed --annotate refFlat.txt --fasta ~ucsc.hg19.fasta --access access-5k-mappable.hg19.bed --output-reference ref.cnn --output-dir --drop-low-coverage

and then: cnvkit.py call SAMPLE.cns

ADD REPLYlink written 24 days ago by biobiu90

This is expected. CNVkit doesn't directly subtract the normal from the test sample; the normal sample is one of several factors that go into the final calls.

ADD REPLYlink written 5 days ago by Eric T.2.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 679 users visited in the last hour