NAME
bamfixflags.py - filter readgroup(s) from a BAM file
SYNOPSIS
bamfixflags.py [-h] [-i BAM] -l FILE [-n INT] [-S] [-b] [-u]
DESCRIPTION
filter readgroup(s) from a BAM file
OPTIONS
optional arguments:
- -h, --help
-
show this help message and exit
- -i BAM, --input BAM
-
Input BAM file
- -l FILE, --lib_info FILE
-
SVTyper JSON file of library information
- -n INT
-
Output first n alignments and quit
- -S
-
Input is SAM format
- -b
-
Output BAM format
- -u
-
Output uncompressed BAM format (implies -b)
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.