BAMRESET(1)

🎀 BAMRESET(1) — General Commands Manual 🎀

okay bestie, buckle up 💖 this is bamreset, from the BAMRESET(1) page in the General Commands Manual, and it's literally the "undo my alignment era" tool. no cap.

✨ NAME ✨

bamreset — reset BAM file to unaligned state 🦋

🌸 SYNOPSIS 🌸

bamreset [options]

💅 DESCRIPTION 💅

bamreset reads a BAM file from standard input, transforms it into a pre-aligned state, and writes the resulting data to standard output as a BAM file. it's giving factory reset but make it genomics ✨

Resetting the file involves the following actions, and bestie, it does ALL of them:

• Remove all SQ lines from the header.
• Set the sorting order to unknown.
• Drop all non primary alignments.
• Remove all auxiliary fields.
• Mark all reads as unmapped and erase the mapping coordinates and template length fields.
• Move all reads to the forward direction by applying reverse complements as necessary such that afterwards no reverse complement flags are set.

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=<1> — 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 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.
• resetheadertext — file name for replacement SAM header. By default the header of the input SAM/BAM/CRAM file is filtered.
• exclude=<SECONDARY,SUPPLEMENTARY> — Do not include reads in the output that have any of the given flags set. The flags are given separated by commas. Valid flags are:
  • PAIRED — read was paired in sequencing
  • PROPER_PAIR — read has been mapped as part of a proper pair
  • UNMAP — read was not mapped
  • MUNMAP — mate of read was not mapped
  • REVERSE — read was mapped to the reverse strand
  • MREVERSE — mate of read was mapped to the reverse strand
  • READ1 — read was first read of a pair during sequencing
  • READ2 — read was second read of a pair during sequencing
  • SECONDARY — alignment is secondary, i.e. an alternative mapping to the primary alignment in the same file
  • QCFAIL — read as marked as having failed quality control
  • DUP — read is marked as a duplicate of another read in the same file (see bammarkduplicates)
  • SUPPLEMENTARY — read is marked as supplementary alignment
• resetaux=<0|1> — auxiliary fields (default).
• resetsortorder=<0|1> — set sort order to unknown if resetsortorder=1 (default) and leave as it is in the input if resetsortorder=0.
• auxfilter=<> — comma separated list of aux tags to be kept if resetaux=0. If the key is not set when resetaux=0, then all tags are kept.

👑 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. 🫶 (fr fr, it says that, don't come for me)

okay that's the whole vibe, bestie — this page came from the BIOBAMBAM source, dated July 2013, and it's still serving BAMRESET(1) realness to this day 💖✨ no cap, go reset something 🦋