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)