NAME¶

bamleftalign - Left-aligns and merges the insertions and deletions in all alignments

SYNOPSIS¶

[BAM data stream] | bamleftalign [options]

DESCRIPTION¶

Left-aligns and merges the insertions and deletions in all alignments in stdin. Iterates until each alignment is stable through a left-realignment step.

OPTIONS¶

-f --fasta-reference FILE

FASTA reference file to use for realignment (required)

-d --debug

Print debugging information about realignment process

-s --suppress-output

Don't write BAM output stream (for debugging)

-m --max-iterations N

Iterate the left-realignment no more than this many times

-c --compressed

Write compressed BAM on stdout, default is uncompressed

AUTHOR¶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.