BAMFIXFLAGS.PY

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.