To generate the segmentation file with copy-number variants, you can use CNV callers that compare the tumor coverage to the normal coverage, to infer relative somatic copy-number events. For example, VarScan's copynumber.
You don't need the MAF file to run ABSOLUTE, if you have the MAF it will be used with the detected copy number and cellularity to compute the cancer cell fraction of the mutations. Useful to infer sample heterogeneity.
I found the current state of ABSOLUTE a bit lacking for exome, it does not provide allele specific copy number, and it does not correlate well with results of SNParray of the same samples.
I know that a newer "component" of ABSOLUTE, called CapSeg, will be available shortly. It will take care of the segmentation in an alleles specific way, similarly to how ABSOLUTE handle the SNP array data. However I've only seen it cited in papers, not real sign of it.
So far the best approach is to use VarScan2, segment the resulting binned depth ratio with DNAcopy or copynumber from bioconductor and then feed the segments to ABSOLUTE.
You could try also a different sofware: Sequenza. It returns allele specific copy number detecting cellularity and ploidy.
For future reference, the program THetA is designed to infer tumor purity, subclone cellularity, and the absolute copy number of segments in the tumor cell clonal/subclonal populations. The program itself is simple to use: The inputs are the tumor BAM, normal BAM, and copy number segments inferred by a third-party program of your choice.
I have exome data for my tumor and match normals. I also have list of the variants with the frequency of the ALT ALLELE for both tumor and normal samples. I want to use ABSOLUTE just to understand the tumor purity percentage and then use that information for somatic variant calling using VarScan, can anyone suggest a working example how to use it as it is not perfectly clear from the Broad webpage how to use it , does anyone has some working example as I cant find one, I just want to understand the tumor purity for my samples. I would be glad if someone can help.
I just downloaded the package, and could not find documentation on this either. It may be worth trying to contact the package maintainer, Jeff Gentry firstname.lastname@example.org as listed in the description file.
Presumably this is too late to be helpful but in case anyone else comes across this - I haven't had anything to do with absolute for a very long time. You'll probably want to contact Scott Carter (email@example.com) with any issues.
Hi Christian, are you finally successful in running ABSOLUTE?
Has anyone tried to this version of Capseg?
It seems like there is no instruction for running CapSeg.
There are no decent instructions for running most software developed by the Broad Institute. They should really read the edgeR vignette sometime, to see how it's done.
You mean the software which is incomplete and hasn't been maintained in the past 3 years? No.