NAME

       samtools-quickcheck - a rapid sanity check on input files

SYNOPSIS

       samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ]

DESCRIPTION

       Quickly  check  that  input  files  appear to be intact. Checks that beginning of the file
       contains a valid header (all formats) containing at least one  target  sequence  and  then
       seeks  to  the  end of the file and checks that an end-of-file (EOF) is present and intact
       (BAM and CRAM only).

       Data in the middle of the file is not read since that would be much more  time  consuming,
       so  please  note  that this command will not detect internal corruption, but is useful for
       testing that files are not truncated before performing more intensive tasks on them.

       This command will exit with a non-zero exit code if any input files  don't  have  a  valid
       header  or are missing an EOF block. Otherwise it will exit successfully (with a zero exit
       code).

OPTIONS

       -v      Verbose output: will additionally print the names of all input  files  that  don't
               pass  the  check  to  stdout.  Multiple  -v options will cause additional messages
               regarding check results to be printed to stderr.

       -q      Quiet mode: disables warning messages on stderr about files that fail.  If both -q
               and -v options are used then the appropriate level of -v takes precedence.

       -u      Expect unmapped input data, so do not require targets in the header.

AUTHOR

       Written by Josh Randall from the Sanger Institute.

SEE ALSO

       samtools(1)

       Samtools website: <http://www.htslib.org/>