CNVKIT scatter --range-list

Question

[nina.naitatmane]

hello, 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.

Thank you

Answer 1

[Eric T.]

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.