DragonFly On-Line Manual Pages

htsfile(1)                   Bioinformatics tools                   htsfile(1)

NAME
       htsfile - identify high-throughput sequencing data files

SYNOPSIS
       htsfile [-chHv] FILE...

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.

       The following options are accepted:

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

       -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)

htslib-1.3                     15 December 2015                     htsfile(1)