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

# bamfillquery(1)

fill query sequences into BAM files

## NAME

bamfillquery - fill query sequences into BAM files

## SYNOPSIS

**bamfillquery** \[options\] \<in.bam queries.fasta \>out.bam

## DESCRIPTION

bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data to a SAM/BAM/CRAM file. Both the alignment input file and the FastA file need to be sorted by query name. See bamsort or bamsormadup for sorting the SAM/BAM/CRAM file to this order.

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.

**I=\<\[stdin\]\>:** input filename, standard input if unset.

**O=\<\[stdout\]\>:** output filename, standard output if unset.

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

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

**reference=\<\[\]\>:** reference FastA file for inputformat=cram and outputformat=cram. An index file (.fai) is required.

## AUTHOR

Written by German Tischler.

## REPORTING BUGS

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

## COPYRIGHT

Copyright © 2009-2016 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.