Question: Absolute Copy Number from low pass WGS
gravatar for senowinski
3.8 years ago by
European Union
senowinski30 wrote:

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?


sequencing snp genome • 1.9k views
ADD COMMENTlink modified 21 months ago by dineika_chandra10 • written 3.8 years ago by senowinski30
gravatar for dineika_chandra
21 months ago by
dineika_chandra10 wrote:

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

ADD COMMENTlink modified 21 months ago • written 21 months ago by dineika_chandra10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1061 users visited in the last hour