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