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