cnv-seq - what do I set the --ref parameter to?

[david_d]

I am trying to detect cnv's in a bam file of an entire human genome using cnv-seq. I was able to create the "hits" file from the bam file using samtools view.

My problem is that I do not know what to put in for the --ref parameter. From what I understand I need to have a hits file from the human reference genome. I have the human reference genome in fasta file format but that will not help me to make a "hits" file. What do I do?

Thank you in advance for your help!

David

[vbajic]

My problem is that I do not know what to put in for the --ref parameter. From what I understand I need to have a hits file from the human reference genome. I have the human reference genome in fasta file format but that will not help me to make a "hits" file. What do I do?

Thank you in advance for your help!
David

I was looking for the explanation of parameters in CNV-seq and I came across your post.
I guess it's already way too late for the answer... however it might be useful to someone.

--ref should be another hits file. For that you need to have another genome sequenced and same as for your --test you need to map the reads to the same reference genome and extract hits file. CNV-seq will compare coverage for --ref and --test hits files. You can download raw sequence reads from for example NCBI site

Ideally for your purpose would be to have raw sequence reads from same human reference as the one you have in fasta file and onto which you mapped your reads.

Cheers!