BAMFLAGSPLIT(1)

🎀 NAME 🎀

bamflagsplit — sort BAM files by coordinate or query name ✨

🌸 SYNOPSIS 🌸

bamflagsplit [options]

🦋 DESCRIPTION 🦋

okay bestie, here's the whole vibe: bamflagsplit reads a name collated BAM, SAM or CRAM file and then distributes all the reads inside it into a whole set of BAM files. like a sorting hat but for sequencing reads, and honestly? it ate 💅

here's exactly where everything lands:

• single — single end reads get placed in the single file
• unmapped — (partially) unmapped read pairs (pairs where at least one of the two mates is unmapped) get placed in the unmapped file
• orphan — orphan reads (pairs where the other mate is missing in the file 😭) get placed in the orphan file
• supplementary — supplementary mappings (mappings which have the supplementary flag set) get placed in the supplementary file
• split — split pair reads (pairs such that the two ends map to different reference sequences/chromosomes) get placed in the split file
• samestrand — read pairs such that both ends map to the same strand get placed in the samestrand file
• improper — improperly mapped read pairs (read pairs where the mapped as a proper pair flag is not set) get placed in the improper file
• proper — properly mapped pairs get placed in the proper file 👑

the following key=value pairs can be given:

• I=<[stdin]> — input filename, and it's standard input if you leave it unset
• level=<-1|0|1|9|11> — set the compression level of the output BAM files. 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 (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:

• 11: igzip compression

• verbose=<1> — valid values are:
  • 1: print progress report on standard error
  • 0: do not print progress report
• disablevalidation=<0|1> — sets whether input validation is performed. valid values are:
  • 0: validation is enabled (default)
  • 1: validation is disabled
• single=<filename> — file name for the single file
• singlemd5=<0|1> — md5 checksum creation for the single output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the splitmd5filename key is set, then the checksum is written to the given file. if splitmd5filename, then no checksum will be computed.
• unmapped=<filename> — file name for the unmapped file
• unmappedmd5=<0|1> — md5 checksum creation for the unmapped output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the splitmd5filename key is set, then the checksum is written to the given file. if splitmd5filename, then no checksum will be computed.
• orphan=<filename> — file name for the orphan file
• orphanmd5=<0|1> — md5 checksum creation for the orphan output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the splitmd5filename key is set, then the checksum is written to the given file. if splitmd5filename, then no checksum will be computed.
• supplementary=<filename> — file name for the supplementary file
• supplementarymd5=<0|1> — md5 checksum creation for the supplementary output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the splitmd5filename key is set, then the checksum is written to the given file. if splitmd5filename, then no checksum will be computed.
• split=<filename> — file name for the split file
• splitmd5=<0|1> — md5 checksum creation for the split output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the splitmd5filename key is set, then the checksum is written to the given file. if splitmd5filename, then no checksum will be computed.
• samestrand=<filename> — file name for the samestrand file
• samestrandmd5=<0|1> — md5 checksum creation for the samestrand output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the samestrandmd5filename key is set, then the checksum is written to the given file. if samestrandmd5filename, then no checksum will be computed.
• improper=<filename> — file name for the improper file
• impropermd5=<0|1> — md5 checksum creation for the improper output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the impropermd5filename key is set, then the checksum is written to the given file. if impropermd5filename, then no checksum will be computed.
• proper=<filename> — file name for the proper file
• propermd5=<0|1> — md5 checksum creation for the proper output file. valid values are:
  • 0: do not compute checksum. this is the default.
  • 1: compute checksum. if the propermd5filename key is set, then the checksum is written to the given file. if propermd5filename, then no checksum will be computed.
• inputformat=<bam> — input file format. all versions of bamflagsplit 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. (genius behaviour, no cap 🫶)

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de>

📜 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.

fr fr, read that last line again — NO WARRANTY, bestie, so back up your files 💀

that's the whole page!! this one came from the BIOBAMBAM crew and it's dated June 2014. go forth and split some reads, you absolute icon 🌈⭐