This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Absolute Copy Number from low pass WGS

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!

genome sequencing snp
• 3,542 views • link
updated by dineika_chandra • dineika_chandra • written by senowinski • senowinski

1 answer

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

• 0 views • link
written by dineika_chandra • dineika_chandra

Log in to answer this question.

More posts like this