BAMCAT(1)

👑 hey bestie, welcome to bamcat(1) 👑

okay so this is bamcat, and it lives in the General Commands Manual section of your terminal, which is lowkey the most iconic section. it concatenates BAM files. that's the whole vibe. let's get into it 💅

✨ NAME ✨

bamcat — concatenate BAM files 🧬

🌸 SYNOPSIS 🌸

bamcat [options]

🦋 DESCRIPTION 🦋

okay so here's the tea: bamcat reads a whole set of input BAM files, merges their headers together, concatenates all the alignment data, and then writes the output to standard output in BAM format. it's giving "one big BAM, please." ✨

you can tell it which input files you want with the I key. and also — plot twist — any none key=value arguments you drop after the key=value pairs will also be treated as input files. so yeah, flexible fr fr.

here are all the key=value pairs you can give it 👇

• I=<stdin> — name of the input file. this key can be used multiple times, so go off, stack them up 💖
• level=<-1|0|1|9|11> — sets the compression level of the output BAM file. the 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

and if libmaus has been compiled with support for igzip (peep <https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data>), then there's one more valid value:

• 11: igzip compression

• verbose=<1> — the 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 get created in the current directory.
• md5=<0|1> — md5 checksum creation for the output file. the 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 the output file. the 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.
• streaming=<0> — streaming mode inactive or active. by default streaming mode is inactive. the valid values are:
  • 0: streaming mode is inactive. only one input file will be opened at any single time, but each input file is openend twice (once for reading the header only, the second time for extracting the alignment data). yeah, twice. she's thorough. 🙈
  • 1: streaming mode is active. all input files will be opened at the same time and kept open until data processing is finished. each input file will be opened only once.

💜 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. 🫡

and that's the whole page, bestie!! this one came from the BIOBAMBAM era, dated October 2013 — yes she's vintage, and yes she still ate. go merge some BAMs. periodt. 💖✨🎀