bamalignfrac1
Compute fraction of aligned bases in alignment file
Usage
bamalignfrac [options]
<input.bam>
Overview
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
*
|
the number of names passing a given regex filter |
|---|---|
*
|
the number of primary alignments |
*
|
the number of total alignments |
*
|
the total number of bases |
*
|
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 |
*
|
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.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).