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.