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
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
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