CNVkit with Ultra Low Pass Samples

Question

[contact]

Hi, I am wondering if CNVkit can be used on ultra low pass WGS samples (depth of coverage of 0.1x - 0.3x)? We are currently looking at using ichorCNA to do that type of CNV analysis, but have used CNVkit up till now for higher depth of coverages, and are wondering if we could just stick with CNVkit to do it.

Thanks

Answer 1

[dineika_chandra]

CNVkit is designed to analyze targeted sequencing data (whole-exome or custom capture). For your purpose, ichorCNA would be quite suited as it was tailored for very low coverage sparse counts across the genome.