NAME

       htsfile - identify high-throughput sequencing data files

SYNOPSIS

       htsfile [-chHv] FILE...
       htsfile --copy [-v] FILE DESTFILE

DESCRIPTION

       The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified
       files are, and provides minimal viewing capabilities for some kinds of data file.

       It can identify sequencing data files such as SAM, BAM, and CRAM; variant calling data files such as  VCF
       and BCF; index files used to index these data files; and compressed versions of many of them.

       For  each  FILE  given, htsfile prints a description of the file format determined, using similar keyword
       conventions to file(1): "text" indicates a textual file that can probably be viewed on a terminal; "data"
       indicates  binary  data; "sequence", "variant calling", and "index" indicate different categories of data
       file.  When it can be identified, the name of the particular file format (such  as  "BAM"  or  "VCF")  is
       printed at the start of the description.

       When  used  to view file contents as text, htsfile can optionally show only headers or only data records,
       but has no other filtering capabilities.  Use samtools or bcftools if you need more extensive viewing  or
       filtering capabilities.

       Alternatively, when --copy is used, htsfile takes exactly two arguments and performs a byte-for-byte copy
       from FILE to DESTFILE.  This is similar  to  cp(1),  but  HTSlib's  remote  file  access  facilities  are
       available for both source and destination.

       The following options are accepted:

       -c, --view
           Instead  of  identifying  the  specified files, display a textual representation of their contents on
           standard output.

           By default, --view refuses to display files in unknown formats.  When --verbose is  also  given,  the
           raw  contents  of  such  files  are  displayed,  with non-printable characters shown via C-style "\x"
           hexadecimal escape sequences.

       -C, --copy
           Instead of identifying or displaying the specified files, copy the source  FILE  to  the  destination
           DESTFILE.  Only --verbose may be used in conjunction with --copy.

       -h, --header-only
           Display data file headers only.  Implies --view.

       -H, --no-header
           When viewing files, display data records only.

       -v, --verbose
           Display  additional  warnings and diagnostic messages.  Using --verbose repeatedly further raises the
           verbosity.

SEE ALSO

       bcftools(1), file(1), samtools(1)