---
name: "bamtagconversion"
section: "1"
platform: "linux"
package: "biobambam2"
version: "2.0.185+ds-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bamtagconversion"
---

# bamtagconversion(1)

convert old tags to new ones

## NAME

bamtagconversion - convert old tags to new ones

## SYNOPSIS

**bamtagconversion** \[options\]

## DESCRIPTION

**bamtagconversion** converts the old MS, MT and MC tags into the corresponding ms, mt and mc tags.  As there is an official MC:Z tag in the SAM spec, **bamtagconversion** only converts MC:i tags. **bamtagconversion** takes a BAM file as an input and outputs a BAM file with the changes made.

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

- \-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=\<0\|1\>:** Valid values are

- 0:

  do not print progress report (default).

- 1:

  print progress report to standard error.

**md5=\<0\|1\>:** md5 checksum creation for output file. This option can only be given if outputformat=bam. Then 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.

**outputthreads=\<\[1\]\>:** output helper threads.

## AUTHOR

Written by Andrew Whitwham.

## REPORTING BUGS

Report bugs to \<aw7@sanger.ac.uk\>

## COPYRIGHT

Copyright © 2015 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.