I'm trying to run ABSOLUTE v 1.0.6 on my tumor exome seq + copy number data. The copy numbers are inferred from low-pass was and I generated somatic mutation calls using mutect and converted to MAF with @Cyriac Kandoths excellent converter. When I run ABSOLUTE using the CNV data only, it's all file and gives me nice output.
However, when I add the MAF file, it breaks saying
Error in CreateMutCnDat(maf, seg.dat, min.mut.af, verbose = verbose) : Malformed MAF file, no ref column supplied
In the source code of ABSOLUTE I understand that I need columns for number of reads supporting the ref and alt alleles which makes perfect sense since it need to estimate frequencies and their variability.
My issue is that I don't have these columns. The MAF spec doesn't mention them (https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%...) and I unable to find any info on what kind of MAF files absolute wants.
So, two questions if anyone has insight:
- Is MAF still the way to go when using SNV data in ABSOLUTE? Is development ongoing using VCF?
- Which columns should be added to the MAF for compatibility with ABSOLUTE? I have VCF files with all info on counts etc, and the BAMs if I need further info.
I also posted at the Broad Cancer Help forum, but that seems to be a low-activity forum compared to biostars.