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 <tischler@mpi-cbg.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.