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

# bamreset(1)

reset BAM file to unaligned state

## NAME

bamreset - reset BAM file to unaligned state

## SYNOPSIS

**bamreset** \[options\]

## DESCRIPTION

bamreset reads a BAM file from standard input, transforms it to a pre aligned state and writes the resulting data to standard output as a BAM file.

Resetting the file involves the following actions:

-

  Remove all SQ lines from the header.

-

  Set the sorting order to unknown

-

  Drop all non primary alignments

-

  Remove all auxiliary fields

-

  Mark all reads as unmapped and erase the mapping coordinates and template length fields

-

  Move all reads to the forward direction by applying reverse complements as necessary such that afterwards no reverse complement flags are set.

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.

**resetheadertext** file name for replacement SAM header. By default the header of the input SAM/BAM/CRAM file is filtered.

**exclude=\<SECONDARY,SUPPLEMENTARY\>:** Do not include reads in the output that have any of the given flags set. The flags are given separated by commas. Valid flags are:

- PAIRED:

  read was paired in sequencing

- PROPER\_PAIR:

  read has been mapped as part of a proper pair

- UNMAP:

  read was not mapped

- MUNMAP:

  mate of read was not mapped

- REVERSE:

  read was mapped to the reverse strand

- MREVERSE:

  mate of read was mapped to the reverse strand

- READ1:

  read was first read of a pair during sequencing

- READ2:

  read was second read of a pair during sequencing

- SECONDARY:

  alignment is secondary, i.e. an alternative mapping to the primary alignment in the same file

- QCFAIL:

  read as marked as having failed quality control

- DUP:

  read is marked as a duplicate of another read in the same file (see bammarkduplicates)

- SUPPLEMENTARY:

  read is marked as supplementary alignment

**resetaux=\<0\|1\>:** auxiliary fields (default).

**resetsortorder=\<0\|1\>:** set sort order to unknown if resetsortorder=1 (default) and leave as it is in the input if resetsortorder=0.

**auxfilter=\<\>:** comma separated list of aux tags to be kept if resetaux=0. If the key is not set when resetaux=0, then all tags are kept.

## 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.