Question: Is there a way to use CNVkit without a reference from normal samples?
gravatar for leandro.bispo.oliveira
2.3 years ago by

I am currently trying to find the CNV in some WGS data.

Is there a command to run CNVkit on a .bam data without using a Reference from Normal Samples?

sequence cnvkit • 1.4k views
ADD COMMENTlink modified 2.3 years ago by h.mon30k • written 2.3 years ago by leandro.bispo.oliveira0

As far as i know, CNV requires reference genome. If you do not have a reference available, you can either build a de novo reference from your reads or find closest species whose reference file is available.

ADD REPLYlink written 2.3 years ago by arta580

He is not asking about a reference genome, he is asking about reference (normal) samples.

ADD REPLYlink written 2.3 years ago by h.mon30k
gravatar for h.mon
2.3 years ago by
h.mon30k wrote:

Create a “flat” reference which assumes equal coverage in all bins by using the --normal/-n flag without specifying any additional BAM files: batch *Tumor.bam -n -t my_baits.bed -f hg19.fasta \
    --access data/access-5kb-mappable.hg19.bed \
    --output-reference my_flat_reference.cnn -d example2/

See further comments here.

ADD COMMENTlink written 2.3 years ago by h.mon30k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 611 users visited in the last hour