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ABSOLUTE input segmentation file
I am writing to seek your help in running ABSOLUTE for tumor-normal pairs for Zebrafish reference genome. We are interested in getting the tumor ploidy.
I have the segmentation file and the mutation file (output from MuTect).After loading the package in R , I follow the steps to run ABSOLUTE (with default options) mentioned at:
RunAbsolute("Sample_BC06_seg.dat",sigma.p="0",max.sigma.h ="0.015", min.ploidy="0.95",max.ploidy="10",primary.disease = "melanoma", platform = 'Illumina_WES', sample.name = "BC06", results.dir = "BC06_output", max.as.seg.count = "1500", max.non.clonal = "0.05" , max.neg.genome = "0", copy_num_type ="allelic", maf.fn="Sample_BC06_Sample_BC12_MuTect_filtered.vcf", min.mut.af = "0", output.fn.base=NULL, verbose=TRUE)
Error: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘Sample_BC06_seg.dat’ has magic number 'Chrom'
Use of save versions prior to 2 is deprecated
See attached Segmentation file
Could you please let me know if I missed something here.
Appreciate all the help.