BAMVALIDATE(1)

📦 version 2.0.185, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 BAMVALIDATE — validating your BAM like the queen you are 💖

okay so bestie, this is bamvalidate from the General Commands Manual section (that's section 1, the "commands you just type" section, iykyk). Buckle up, we're doing alignment validation today and honestly it's giving main character energy. ✨

🌸 NAME 🌸

bamvalidate — validate BAM file. that's it. that's the whole job. no cap. 💅

🦋 SYNOPSIS 🦋

bamvalidate [options]

like, that's the entire usage. options only, no positional args, we love a clean interface.

👑 DESCRIPTION 👑

bamvalidate reads a BAM, SAM or CRAM file and checks the alignments inside it for validity. that's the vibe check. 🫶

if all the alignments in the source file pass validation, the program exits with code 0. if not? non-zero exit code, and honestly it deserved it. 😭

by default, no data is produced on the standard output channel. but if you set the passthrough parameter to 1, then the alignments get recoded to standard output according to whatever output parameters you gave it. slay.

the following key=value pairs can be given:

  • verbose=<0|1> — print stats or don't. valid values are:
    • 1: print statistics on the standard error channel at the end of a successful run
    • 0: do not print statistics
  • passthrough=<0|1> — recode alignments to standard output if passthrough=1. default is passthrough=0.
  • 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 there's one more valid value:

  • 11: igzip compression
  • tmpfile=<filename> — set the prefix for temporary file names.
  • md5=<0|1> — md5 checksum creation for the output file. this option can only be given if outputformat=bam. 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. this option can only be given if outputformat=bam. 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 output BAM index if index=1.
  • inputformat=<bam> — input file format. all versions of bamsort come with support for the BAM input format. if the program is in addition linked to the io_lib package, then the following options are valid:
  • outputformat=<bam> — output file format. all versions of bamsort come with support for the BAM output format. if the program is in addition linked to the io_lib package, then the following options are valid:
  • I=<[stdin]> — input filename, standard input if unset.
  • O=<[stdout]> — output filename, standard output if unset.
  • inputthreads=<[1]> — input helper threads, only valid for inputformat=bam.
  • outputthreads=<[1]> — output helper threads, only valid for outputformat=bam.
  • reference=<[]> — reference FastA file for inputformat=cram and outputformat=cram. an index file (.fai) is required. don't forget it bestie, it will simply not work. 🙈
  • range=<> — input range to be processed. this option is only valid if the input is a coordinate sorted and indexed BAM file.
  • basequalhist=<[0]> — compute base quality histogram and output this histogram on the standard error channel after a successful validation run. the histogram lines are prefixed with [H]. there is one line for each occurring base quality value, and two lines at the end specifying the minimum and maximum occurring quality value. the lines contain tabulator symbol separated columns.

the occurring base quality lines have 5 columns after the [H] column. these designate:

  1. the numerical quality level
  2. the ASCII character representation of this level (e.g. ! for quality 0 or I for 40)
  3. the absolute number of occurrences of the value
  4. the fraction of the occurrences of the value (the absolute number for this value divided by the sum of the occurrences over all values)
  5. the cumulative fraction for all values up to and including the current value

the minimum and maximum value lines have min and max respectively in the second column. the third and fourth column contain the numerical value and the ASCII representation of this value. for all lines the ASCII representation of a base quality value may be empty if the numerical quality value does not correspond to a printable ASCII code. it's giving ghost column, iconic. ✨

💜 AUTHOR 💜

written by German Tischler. periodt. 👑

🎀 REPORTING BUGS 🎀

report bugs to <germant@miltenyibiotec.de> — be nice, be specific, include the receipts. 🫶

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, so pls don't come for anyone. 💀

⭐ SEE ALSO ⭐

(no SEE ALSO section in the original, so nothing to link here — go read the PDFs if you're curious, they're literally linked up in inputformat and outputformat.)

that's the whole page, you're validated, you're thriving, go check your BAMs 💖✨🎀🦋🌸💅🫶🔥👑🌈⭐💜

this cutie came to you from BIOBAMBAM, dated October 2014, filed under BAMVALIDATE(1) in the General Commands Manual. byeeee 💕

📦 where this page comes from