arden-filter1

Filter a sam file based on the analysis with arden

Usage

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

Overview

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

Releases

Unchanged in 6 releases since Debian 8 (Jessie).

8–13