BAMFILTERHEADER(1)

✨ NAME ✨

bamfilterheader — filter auxiliary tags from a BAM file 💖 (yes bestie, it's giving spring cleaning for your headers)

She lives in the General Commands Manual section, section 1, and she is so good at her job.

🌸 SYNOPSIS 🌸

bamfilterheader [options]

🎀 DESCRIPTION 🎀

okay so here's the tea 🫖: bamfilterheader reads a BAM file from a file, filters the header, and writes the resulting data to standard output as a BAM file. Iconic behavior, no notes.

Filtering the header means:

• removing sequence (SQ) lines, and
• removing read group (RG) lines

...that are not referenced in any alignment. If nobody's using it, it's not coming to the party. periodt. 💅

⚠️ Heads up bestie: the input file gets scanned twice during the process, so the name of the input file needs to be provided using the I key. No I, no vibes. 😭

The following key=value pairs can be given, where the keep and remove keys are mutually exclusive. Pick a lane, babe. 🚫

• I=<inputfilename> — name of input BAM file. Literally the main character here.
• level=<-1|0|1|9|11> — set the 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

(ngl I keep mine on 1 because I want to know things ✨)

• tmpfile=<filename> — prefix for temporary files. By default the temporary files are created in the current directory. 🏠
• md5=<0|1> — md5 checksum creation for the 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 the 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.

👑 AUTHOR 👑

Written by German Tischler. king behavior, we love to see it 👑

💀 REPORTING BUGS 💀

Report bugs to <germant@miltenyibiotec.de> 📬 (they wanna hear about it, fr fr)

🌈 COPYRIGHT 🌈

Copyright © 2009-2014 German Tischler, © 2011-2014 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. 🫶 (read that again, bestie — NO WARRANTY, okay? 😭)

and that's the whole page!! mwah 💖 this lil beauty comes to you from the BIOBAMBAM collection, dated January 2014, and yeah she's been serving since then ✨🦋 go filter those headers, you absolute icon 🌸