CNVKIT scatter --range-list
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6.8 years ago

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

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6.7 years ago
Eric T. ★ 2.8k

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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