asntech/infer_wgd_pga repository overview

⁠Infer WGD and PGA using FACETS Calls

⁠Infer Whole-genome doubling (WGD)

Infers whole genome doubling based on Bielski CM, Zehir A, Penson AV, et al. Genome doubling shapes the evolution and prognosis of advanced cancers⁠. Calculates major copy number (MCN) estimate based on total copy number (TCN) estimate and minor copy number (LCN) estimate from FACETS and calls whole-genome doubling if the average MCN across the autosomal genome is greater than 2. In cases that LCN is equal to NA, a value of 0 is used.

docker run -it asntech/infer_wgd_pga:v1.0 infer_wgd.py --help

Inputs:

• Copy number cellular fractions

Outputs:

• Fraction major copy number greater than 2
• Putative whole genome doubling, if the fraction of MCN across the autosomal genome is greater than 0.5

Relevant codeblock in WDL⁠

⁠Infer precent genome altered (PGA)

Infers the percentage of the genome altered by copy number alterations (differences from normal ploidy). Commonly used in a variety of papers, (example here⁠). This is done by taking all the segments that do not match diploid copy number (2 for autosomes and 1 for sex chromosomes) and computing their sizes, then dividing by the total size of all the segments. In cases that total copy number is equal to NA, a value of 0 is used, although this should be impossible.

docker run -it asntech/infer_wgd_pga:v1.0 infer_pga.py --help

Inputs:

• Copy number cellular fractions

Outputs:

• Fraction of genome altered

These two scripts to infer WGD and PGA come from: https://github.com/vanallenlab/facets⁠