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

# bamauxmerge(1)

merge information in unmapped and mapped alignment files

## NAME

bamauxmerge - merge information in unmapped and mapped alignment files

## SYNOPSIS

**bamauxmerge** \[options\] in\_unmapped in\_mapped

## DESCRIPTION

bamauxmerge reads and merges two SAM/BAM/CRAM files which are expected to have the following properties:

- \*

  the first file contains only unmapped reads and it's header contains no SQ lines

- \*

  the second file was produced by an aligner based on the content of the first file.

- \*

  the order of the reads is the same in the first an second file into a single alignment file.

The headers of the two files are merged in the following file:

- \*

  the SQ lines contained in the header of the second file are appended to the header of the first file to obtain the header of the output file

- \*

  all other header information from the second file is discarded

The output records are constructed in the following way:

- 1\.

  Take a record from the second file

- 2\.

  Copy all aux fields from the corresponding record in the first file which are not already present.

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=\<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.

**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:

- bam:

  BAM (see http://samtools.sourceforge.net/SAM1.pdf)

- sam:

  SAM (see http://samtools.sourceforge.net/SAM1.pdf)

- cram:

  CRAM (see http://www.ebi.ac.uk/ena/about/cram\_toolkit)

**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:

- bam:

  BAM (see http://samtools.sourceforge.net/SAM1.pdf)

- sam:

  SAM (see http://samtools.sourceforge.net/SAM1.pdf)

- cram:

  CRAM (see http://www.ebi.ac.uk/ena/about/cram\_toolkit). This format is not advisable for data sorted by query name.

**inputthreads=\<\[1\]\>:** input helper threads, only valid for inputformat=bam.

**outputthreads=\<\[1\]\>:** output helper threads, only valid for outputformat=bam.

## AUTHOR

Written by German Tischler.

## REPORTING BUGS

Report bugs to \<germant@miltenyibiotec.de\>

## COPYRIGHT

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.