Provided by: tabix_1.7-2_amd64 
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.
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.
-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)