The CTCallR is an R package destined at calling chromothripsis from whole-genome sequencing data. It applies a series of tests proposed in Korbel & Campbell, Cell, 2013 to annotate high-density-breakpoint regions as "clusters of breakpoints" or (likely) "chromothripsis".
It expects the user to have run a copy-number and structural variant caller and format their output properly.
An example output figure is shown below:
You can install the package with devtools in an R session:
devtools::install_github("VanLoo-lab/CTCallR", build_opts = c("--no-build-vignettes"))
The package relies on a few dependencies, nameley the R packages: vcf, MASS, copynumer, parallel, EMT.
It also relies on the circos software to plot the results.
Please see also ShatterSeek, for another chromothripsis caller used in The Pan-Cancer Analysis of Whole Genomes (PCAWG) study.
The main functions require two input files: copy-number calls across samples, as well as structural variant calls across samples.
Ideally, copy-number calls should have been informed with the structural variants to identify the copy-number breakpoints, as is done in Battenberg.
Example files are given in the example_input directory for both input file types.
For the copy number calls a tsv file, where the rows represent genomic segments, with the following columns in that order:
samplename: the name of the sample in which this segment has been characterized
chr: the chromosome of that segment
startpos : the start position of that segment
endpos : the end position of that segment
nMaj1_A : the number of copies of the major allele
nMin1_A : the number of copies of the minor allele
frac1_A: the fraction subclonal (leave as 1 if no subclonality information)
For the structural variant calls, a tsv file, where the rows represent pairs of structural variant breakpoints, with columns in that order:
samplename : the name of the sample in which this sv has been characterized
chr1 : the first chromosome of the pair
pos1 : the position on that first chromosome of the pair
chr2 : the second chromosome of the pair
pos2 : the position on that second chromosome of the pair
class : the type of sv (can be extracted from most sv callers with strand and mapping info), either of the type head-to-head inversion, tail-to-tail inversion, tandem duplication, deletion or translocation.
To test CTCallR, we propose example data from 3 sarcomas of the ICGC PCAWG UK cohort.
See documentation for example run. In an R session, type:
?CTCallR