I would like to use this tool with whole genome sequencing, germline data and haploid organisms. What parameters would be more suitable? Regarding the segmentation method, would be better cbs, hmm or hmm-germline method? and with the call command, which parameter would be better, -m threshold (t=-1.0, 0.5849625, 1.3219281, 1.8073549, 2.1699250) or -m clonal. Finally, If I don't have normal samples, it would be better to make a flat reference file or to choose some samples to make the reference?
Hello,
I would like to use this tool with whole genome sequencing, germline data and haploid organisms. What parameters would be more suitable? Regarding the segmentation method, would be better cbs, hmm or hmm-germline method? and with the call command, which parameter would be better, -m threshold (t=-1.0, 0.5849625, 1.3219281, 1.8073549, 2.1699250) or -m clonal. Finally, If I don't have normal samples, it would be better to make a flat reference file or to choose some samples to make the reference?
Thanks