---
name: "fitgcp"
section: "1"
platform: "linux"
package: "fitgcp"
version: "0.0.20150429-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fitgcp"
---

# fitgcp(1)

fit mixtures of probability distributions to genome coverage profiles

## 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**, **--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