bammerge - merge BAM files
bammerge [options]
bammerge reads a set of input BAM files, merges the contained headers and
alignment data and writes the output on standard output in BAM format. The
input files can be specified via the I key. Any none key=value arguments given
after the key=value pairs will also be considered as input files. The input
files need to be sorted by coordinate or query name. The set of reference
sequences in the files does not need to be identical. For merging coordinate
sorted files however the order of the reference sequences in the headers needs
to be consistent among the files, i.e. if reference sequence A appears before
reference sequence B in any input file, then this needs to hold for all other
files as well. If the order is not consistent then bammerge cannot be used for
merging. In this case the merging can be done by concatenating the files using
bamcat and running bamsort afterwards.
The following key=value pairs can be given:
I=<stdin>: name of the input file. This key can be used multiple
times
SO=<coordinate>: Sort order. By default the sort order is
coordinate.
- coordinate:
- input files are sorted by coordinate. The created output
file will be sorted by coordinate as well.
- queryname:
- input files are sorted by query name. The created output
file will be sorted by query name as well.
level=<-1|0|1|9|11>: set compression level of the output BAM file.
Valid values are
- -1:
- zlib/gzip default compression level
- 0:
- uncompressed
- 1:
- zlib/gzip level 1 (fast) compression
- 9:
- zlib/gzip level 9 (best) compression
If libmaus has been compiled with support for igzip (see
https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data)
then an additional valid value is
- 11:
- igzip compression
verbose=<1>: Valid values are
- 1:
- print progress report on standard error
- 0:
- do not print progress report
tmpfile=<filename>: prefix for temporary files. By default the
temporary files are created in the current directory
md5=<0|1>: md5 checksum creation for output file. Valid values are
- 0:
- do not compute checksum. This is the default.
- 1:
- compute checksum. If the md5filename key is set, then the
checksum is written to the given file. If md5filename is unset, then no
checksum will be computed.
md5filename file name for md5 checksum if md5=1.
index=<0|1>: compute BAM index for output file. Valid values are
- 0:
- do not compute BAM index. This is the default.
- 1:
- compute BAM index. If the indexfilename key is set, then
the BAM index is written to the given file. If indexfilename is unset,
then no BAM index will be computed.
indexfilename file name for BAM index if index=1.
IL name of file containing input file names. The given text file contains
a list of input file names, one file per line.
Written by German Tischler.
Report bugs to <
[email protected]>
Copyright © 2009-2013 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.