NAME

bam_quality_stats.pl -- Generates quality statistics from specified BAM input files.

SYNOPSIS

bam_quality_stats.pl --dir <PATH> --bam <file1:file2:..> --odir <PATH> [--match] [--clip] [--qual] [--edit] [--rlib <PATH>] [[--help]

OPTIONS

--dir

Path to directory with BAM files. All BAM files in this directory will be processed.

--bam

List seperated by ':'. Specifies bam files which schould be parsed and processd. Can be combined with --dir.

--odir

Path to output directory. In this directory several output files will be created. Existing files with identiacal names will be over written. Can be combined with --bam.

--match

Provides stats how many bases match the reference genome in the alignment's CIGAR string. If sequence mismatchs are defined as alignment matches depends on the used read mapper. Some use the '=' and the 'X' symbol. In this case only sequencing matches are counted. If the aligner only reports 'M' no distinction between sequence match and mismatch can be done. In any case, clipped bases, deletions, insertions are excluded.

Plot data_match_stats.pdf is created in --odir.

--qual

Provides stats on quality of the read match against the reference sequence.

Plot data_qual_stats.pdf is created in --odir.

--edit

Provides stats on the edit distance between read and mapped reference position.

Plot data_edit_stats.pdf is created in --odir.

--segemehl

Toggles to specific segemehl bam file characteristics (e.g., mapped fragments per line).

--rlib | -r

Path to the R library. Default is '/usr/bin/R'.

--help | -h

Print short help.

--man

Prints the manual page and exits.

--verbose

Prints additional output.

DESCRIPTION

This program screens a given directory for BAM files and computes various statistics on them.

AUTHOR

Fabian Amman <fabian@tbi.univie.ac.at>