Can anyone help me in using the cnvkit scatter command with a range-list?
I tried to use it with a bed file like an argument (-l test.bed) in which each line looks like:
"chr1 115252151 115252273 NRAS_ex4". that didn't work.
If the input is BED, the fields need to be separated by tabs, not spaces. Alternatively, text coordinate ranges like "chr1:115252151-115252273" will work.
In either case you can leave off the gene names, as CNVkit will ignore them and just use the specified region coordinates.
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