BAMFILTERMC(1)

💖 BAMFILTERMC 💖

okay so bestie, welcome to bamfiltermc(1), a little general commands manual page that is lowkey a lifesaver and I'm obsessed with it, let's get into it 🫶

✨ NAME ✨

bamfiltermc — literally just here to remove MC aux fields for reads with unmapped mates 🧹💅

✨ SYNOPSIS ✨

bamfilterflags [options]

(no cap, that's exactly what it says, and yes it says bamfilterflags, we don't make the rules, we just report them 🙈)

✨ DESCRIPTION ✨

So here's the vibe: bamfiltermc reads a SAM/BAM/CRAM file from standard input, removes MC aux fields for reads with unmapped mates — which, btw, were erroneously inserted by earlier versions of biobambam2 (not our fault, we fixed it, slay ✨) — and then writes the resulting alignments out to a SAM/BAM/CRAM file on the standard output stream. In and out, main character energy, periodt. 💖

The following key=value pairs can be given, bestie, write these down 📝:

• level=<-1|0|1|9|11> — sets 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

And 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 there's one more valid value, a little bonus queen:

• 11 — igzip compression

• numthreads=<1> — number of worker threads. 💪
• inputthreads=<1> — number of input threads.
• outputthreads=<1> — number of output threads.
• 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.
• 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. ⚠️
• 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)

👑 AUTHOR 👑

Written by German Tischler. (ty king 🙏)

🐛 REPORTING BUGS 🐛

Found a bug? Not the vibe, but okay, report it 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. 😭 (fr fr, that's what it says)

and that's the whole page bestie, you ate this 🌸💖 this little icon is from the BIOBAMBAM2 era, dated July 2016, and it's still serving. mwah 💅✨🦋