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BAMMDNM(1) General Commands Manual BAMMDNM(1)


bammdnm - compute MD and NM fields


bammdnm [options]


bammdnm reads a coordinate sorted BAM file from standard input, fills the MD and NM auxiliary fields for each mapped read fragment and writes the resulting data to a BAM file on standard output.

The following key=value pairs can be given:

reference=<>: file name of the reference in uncompressed or compressed FastA format. This field is required, i.e. the program will quit if the key is not given. Uncompressed FastA is expected in general FastA file format. A FastA index (.fai file) is required. This index can be created while reformatting the input file using normalisefasta. Compressed FastA can be provided in two forms. The first form is the format generated by the razip program. In this case a razf file and a corresponding FastA index file (.fai) is required. The second form can be generated by normalisefasta using the setting bgzf=1. The index optionally created by normalisefasta when setting the index key is required for bammdnm. The index file has to be stored as ref.fa.bgzf.idx for a compressed reference file name of ref.fa.bgzf.

level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are

zlib/gzip default compression level
zlib/gzip level 1 (fast) compression
zlib/gzip level 9 (best) compression

If libmaus has been compiled with support for igzip (see then an additional valid value is

igzip compression

verbose=<0|1>: print progress report while processing the file. Valid values are

do not print progress report
print progress report (default)

disablevalidation=<0|1>: disable input validation. Valid values are

check validity of input data (default)
do not check validity of input data

tmpfile=<filename>: prefix for temporary files. By default temporary files are created in the current directory.

md5=<0|1>: md5 checksum creation for output file. Valid values are

do not compute checksum. This is the default.
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

do not compute BAM index. This is the default.
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 index file if index=1.

recompindetonly=<0|1>: only compute/recompute MD and NM fields if the read or reference in the relevant region contain indeterminate (non A, C, G or T) bases. Valid values are

compute/recompute all MD and NM fields. This is the default.
only recompute if indeterminate bases are involved

warnchange=<0|1>: warn if values for the MD and NM fields are already present but different from the newly computed ones. Valid values are

do not warn about changes. This is the default.
print a warning message when changing previously stored values

ioblocksize=<128k>: block size used for I/O operations


Written by German Tischler.


Report bugs to <>


Copyright © 2009-2014 German Tischler, © 2011-2014 Genome Research Limited. License GPLv3+: GNU GPL version 3 <>
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

March 2014 BIOBAMBAM