Man page - bamalignfrac(1)
Packages contains this manual
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apt-get install biobambam2
Manual
BAMALIGNFRAC
NAMESYNOPSIS
DESCRIPTION
AUTHOR
REPORTING BUGS
COPYRIGHT
NAME
bamalignfrac - compute fraction of aligned bases in alignment file
SYNOPSIS
bamalignfrac [options] <input.bam>
DESCRIPTION
bamalignfrac reads a SAM/BAM/CRAM file, computes a set of statistical values and outputs these on the standard output channel. The values produced are
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the number of names passing a given regex filter |
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the number of primary alignments |
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the number of total alignments |
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the total number of bases |
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the total number of aligned bases |
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the fraction of aligned bases |
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the total number of clipped/unaligned bases |
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the number of unmapped reads |
These values are printed on the standard output channel at the end of the program run in the last line printed by the program. The program prints a set of line description line prior to that.
The input file needs to be provied in query name sorted order, which can be obtained via e.g.
$ bamsort SO=queryname
right before being passed to bamalignfrac.
The following key=value pairs can be given:
verbose=<0|1>: print preliminary values for file prefixes while processing the input file
name=<>: only consider reads matching the given regular expression. By default all reads are considered.
AUTHOR
Written by German Tischler-Höhle.
REPORTING BUGS
Report bugs to <germant@miltenyibiotec.de>
COPYRIGHT
Copyright ©
2009-2019 German Tischler, © 2011-2013 Genome Research
Limited. License GPLv3+: GNU GPL version 3
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and
redistribute it. There is NO WARRANTY, to the extent
permitted by law.