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

# bamranksort(1)

sort BAM files by rank

## NAME

bamranksort - sort BAM files by rank

## SYNOPSIS

**bamranksort** \[options\]

## DESCRIPTION

**bamranksort** reads a BAM file (preferably in nearly sorted order), sorts it in rank order and then outputs a BAM.

The input BAM file must already have the rank prefix added to the alignment names and any attempt to sort a file without these name prefixes will fail. **bamranksort** also assumes that all alignments of the same name are grouped together (a pair of reads plus any number of supplementary/secondary reads).  If it finds any alignments in a separate group the program will exit.

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=\<0\|1\|2\>:** Valid values are

- 0:

  do not print progress report (default).

- 1:

  print progress report to standard error.

- 2:

  print more values for debugging only to standard error.

**md5=\<0\|1\>:** md5 checksum creation for output file. This option can only be given if outputformat=bam. Then 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.

**misordered=\<500000\>:** number of alignments to accumulate before giving up.

**step=\<2\>:** expected increment between ranks.

**outputthreads=\<\[1\]\>:** output helper threads.

## AUTHOR

Written by Andrew Whitwham.

## REPORTING BUGS

Report bugs to \<aw7@sanger.ac.uk\>

## COPYRIGHT

Copyright © 2015 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.