## 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**,**--help**- show this help message and exit
**-d**DIST,**--distributions**=*DIST*- Distributions to fit. z->zero; n: nbinom (MOM); N: nbinom (MLE); p:binom; t: tail. Default: zn
**-i**STEPS,**--iterations**=*STEPS*- Maximum number of iterations. Default: 50
**-t**THR,**--threshold**=*THR*- Set the convergence threshold for the iteration. Stop if the change between two iterations is less than THR. Default: 0.01
**-c**CUTOFF,**--cutoff**=*CUTOFF*- Specifies a coverage cutoff quantile such that only coverage values below this quantile are considered. Default: 0.95
**-p**,**--plot**- Create a plot of the fitted mixture model. Default: False
**-m**MEAN,**--means**=*MEAN*-
Specifies the initial values for the mean of each
Poisson or Negative Binomial distribution. Usage:
**-m**12.4**-m**16.1 will specify the means for the first two non-zero/tail distributions. The default is calculated from the data. **-a**ALPHA,**--alpha**=*ALPHA*-
Specifies the initial values for the proportion alpha
of each distribution. Usage: For three distributions
**-a**0.3**-a**0.3 specifies the proportions 0.3, 0.3 and 0.4. The default is equal proportions for all distributions. **-l**,**--log**- Enable logging. Default: False
**--view**-
Only view the GCP. Do not fit any distribution.
Respects cutoff (
**-c**). Default: False