NAME

       bamvalidate - validate BAM file

SYNOPSIS

       bamvalidate [options]

DESCRIPTION

       bamvalidate  reads  a  BAM,  SAM  or  CRAM  file  and  checks the contained alignments for
       validity. If all the alignments in the source file pass validation, then the program exits
       with  code  0,  otherwise it exits with a non-zero code. By default no data is produced on
       the standard output channel, if the passthrough parameter is set to 1, then the alignments
       are recoded to standard output according to the given output parameters.

       The following key=value pairs can be given:

       verbose=<0|1>: 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 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

       tmpfile=<filename>: set the prefix for temporary file names

       md5=<0|1>: md5 checksum creation for output  file.  This  option  can  only  be  given  if
       outputformat=bam. Then 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.  This  option  can  only  be  given  if
       outputformat=bam. Then 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 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)

       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.

       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.

       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 in 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 the numerical quality level, the ASCII character representation of
       this  level  (e.g. ! for quality 0 or I for 40), the absolute number of occurrences of the
       value, the fraction of the occurrences of the value (the absolute number  for  this  value
       divided by the sum of the occurrences over all values) and 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.

AUTHOR

       Written by German Tischler.

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.