---
name: "arden-filter"
section: "1"
platform: "linux"
package: "arden"
version: "1.0-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/arden-filter"
---

# arden-filter(1)

filter a SAM file based on the analysis with ARDEN

## NAME

arden-filter - filter a SAM file based on the analysis with ARDEN

## SYNOPSIS

**arden-filter** \[*INPUT SAM*\] \[*OUTPUTFILE*\] \[*OPTIONS*\]...

## DESCRIPTION

Script to filter and a SAM file based on the analysis with ARDEN. It is necessary to specify the desired cutoffs for RQS,GAPS and MM. Type: python filter **-e** 1 for printing some examples.

## OPTIONS

Required Arguments:

- *OUTPUTFILE*

  Outputfilename

- *INPUT*

  Single SAM file to filter.

- **--version**

  show program's version number and exit

- **-h**, **--help**

  show this help message and exit

- **-r** RQS, **--rqs**=*RQS*

  Threshold for minimum read quality score.. \[default: 0\]

- **-m** MM, **--mismatches**=*MM*

  Threshold for maximum number of mismatches in an alignment \[default: 3\]

- **-g** GAPS, **--gaps**=*GAPS*

  Threshold for maximum number of gaps in an alignment. \[default: 3\]

- **-e** PEXAMPLES, **--examples**=*PEXAMPLES*

  set to 1 if you want to print examples