Absolute Copy Number from low pass WGS

Question

[senowinski]

Does anyone know of a method to calculate absolute copy number from low pass WGS? I have low pass human wgs with ~6 million reads, unfortunately it is very low meaning that only the LogR can be calculated and not the b-allele frequency. I am currently using QDNAseq package in R to calculate the logR, but was wondering if there are any other tools to then obtain absolute copy number from this. Does anyone have any suggestions that are not along the lines of just setting a threshold for gains and losses?

Thanks!

Answer 1

[dineika_chandra]

You could use ichorCNA which is a relatively new software geared towards very shallow coverage WGS. It outputs absolute copy number values.

github link

Nature Communications 2017 paper