Provided by: fitgcp_0.0.20150429-1_amd64

**NAME**

fitgcp - fit mixtures of probability distributions to genome coverage profiles

**SYNOPSIS**

fitgcp[options]NAME

**DESCRIPTION**

Fits mixtures of probability distributions to genome coverage profiles using an EM-like iterative algorithm. The script uses a SAM file as input and parses the mapping information and creates a Genome Coverage Profile (GCP). The GCP is written to a file, such that this step can be skipped the next time. The user provides a mixture model that is fitted to the GCP. Furthermore, the user may specify initial parameters for each model. As output, the script generates a text file containing the final set of fit parameters and additional information about the fitting process. A log file contains the the current set of parameters in each step of the iteration. If requested, a plot of the GCP and the fitted distributions can be created.

**OPTIONS**

NAME: Name of SAM file to analyze.-h,--helpshow this help message and exit-dDIST,--distributions=DISTDistributions to fit. z->zero; n: nbinom (MOM); N: nbinom (MLE); p:binom; t: tail. Default: zn-iSTEPS,--iterations=STEPSMaximum number of iterations. Default: 50-tTHR,--threshold=THRSet the convergence threshold for the iteration. Stop if the change between two iterations is less than THR. Default: 0.01-cCUTOFF,--cutoff=CUTOFFSpecifies a coverage cutoff quantile such that only coverage values below this quantile are considered. Default: 0.95-p,--plotCreate a plot of the fitted mixture model. Default: False-mMEAN,--means=MEANSpecifies the initial values for the mean of each Poisson or Negative Binomial distribution. Usage:-m12.4-m16.1 will specify the means for the first two non-zero/tail distributions. The default is calculated from the data.-aALPHA,--alpha=ALPHASpecifies the initial values for the proportion alpha of each distribution. Usage: For three distributions-a0.3-a0.3 specifies the proportions 0.3, 0.3 and 0.4. The default is equal proportions for all distributions.-l,--logEnable logging. Default: False--viewOnly view the GCP. Do not fit any distribution. Respects cutoff (-c). Default: False