---
name: "bamauxmerge2"
section: "1"
platform: "linux"
package: "biobambam2"
version: "2.0.185+ds-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bamauxmerge2"
---

# bamauxmerge2(1)

merge information in unmapped and mapped BAM files

## NAME

bamauxmerge2 - merge information in unmapped and mapped BAM files

## SYNOPSIS

**bamauxmerge2** \[options\] in\_unmapped in\_mapped

## DESCRIPTION

bamauxmerge2 reads and merges two BAM 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.

- \*

  both files are sorted in query name order 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.

- 3\.

  Reinsert clipped adapter bases/quality values stored in the qs/qq by aux fields by fastqtobam2 and remove the qs/qq aux fields while inserting appropriate soft clipping CIGAR operations.

- 4\.

  Fix mate information like bamfixmateinformation.

- 5\.

  Insert the mate CIGAR information fields MC and MS if the mate is aligned.

- 6\.

  Insert the MQ (mate quality) aux field.

The following key=value pairs can be given:

**zz=\<0\|1\>:** replace read name by content of nn aux field. Valid values are

- 1:

  replace read name

- 0:

  do not replace read name

**calmdnm=\<0\|1\>:** recompute MD and NM aux fields. Valid values are

- 1:

  recompute MD and NM aux fields. This requires the calmdnmreference key to be set to the name of an appropriate FastA file.

- 0:

  do not recompute MD and NM aux fields

**calmdnmreference=\<\>:** reference FastA file.

**replacecigar=\<0\|1\>:** replace M cigar operations by the appropriate = and X operations. Valid values are

- 1:

  replace cigar operations. This requires the calmdnmreference key to be set on invocation.

- 0:

  do not replace cigar operations

**hash=\<crc32prod\>:** hash used for computing sequence checksums. See bamseqchksum for further information.

**filehash=\<md5\>:** hash used for computing output file checksums.

**chksumfn=\<\>:** file name used for storing sequence checksum information. By default this information is not saved.

**filehashfn=\<\>:** file name used for storing file checksum information. By default this information is not saved.

**level=\<-1\|0\|1\|9\>:** 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

**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.

**threads=\<\[1\]\>:** number of threads used for processing. By default 1 thread is used. Set to 0 for using as many threads as CPU cores detected.

## AUTHOR

Written by German Tischler.

## REPORTING BUGS

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

## COPYRIGHT

Copyright © 2009-2019 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.