BAMRECALCULATECIGAR(1) | General Commands Manual | BAMRECALCULATECIGAR(1) |
bamrecalculatecigar - concatenate BAM files
bamrecalculatecigar [options]
bamrecalculatecigar reads a SAM/BAM/CRAM file, rewrites the CIGAR strings of aligned reads replacing M operations by = and X operations and writes the resulting data to a SAM/BAM/CRAM file. Unaligned reads are not changed. Rewriting the CIGAR strings requires a reference in FastA format. The path to this FastA file needs to be provided using the reference key. The alignment input file needs to be sorted by coordinate.
The following key=value pairs can be given:
level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are
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
verbose=<1>: Valid values are
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
md5filename file name for md5 checksum if md5=1.
index=<0|1>: compute BAM index for output file. Valid values are
indexfilename file name for BAM index if index=1.
inputformat=<bam>: input file format. All versions of bamsort come with support for the BAM input format. If the program in addition is linked to the io_lib package, then the following options are valid:
outputformat=<bam>: output file format. All versions of bamsort come with support for the BAM output format. If the program in addition is linked to the io_lib package, then the following options are valid:
I=<[stdin]>: input filename, standard input if unset.
O=<[stdout]>: output filename, standard output if unset.
inputthreads=<[1]>: input helper threads, only valid for inputformat=bam.
outputthreads=<[1]>: output helper threads, only valid for outputformat=bam.
reference=<[]>: reference FastA file for inputformat=cram and outputformat=cram. An index file (.fai) is required.
Written by German Tischler.
Report bugs to <germant@miltenyibiotec.de>
Copyright © 2009-2016 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.
February 2016 | BIOBAMBAM |