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

# bamclipXT(1)

reinsert query sequence fragments removed by bamadapterclip

## NAME

bamclipXT - reinsert query sequence fragments removed by bamadapterclip

## SYNOPSIS

**bamclipXT** \[options\]

## DESCRIPTION

bamclipXT processes a SAM/BAM/CRAM file containing the XT flag produced by Picard's MarkIlluminaAdapters and sets the designated base qualities to 2. The original base qualities are copied to a new aux tag named cq (clipped quality). The resulting data is then written as a SAM/BAM/CRAM file.

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

**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.

## 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.