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/>