htsfile(1) Bioinformatics tools htsfile(1)NAMEhtsfile - identify high-throughput sequencing data files
SYNOPSIShtsfile [-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; vari‐
ant 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" indi‐
cates a textual file that can probably be viewed on a terminal; "data"
indicates binary data; "sequence", "variant calling", and "index" indi‐
cate 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 capabili‐
ties. 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 rep‐
resentation 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 --ver‐
bose repeatedly further raises the verbosity.
SEE ALSObcftools(1), file(1), samtools(1)htslib-1.3 15 December 2015 htsfile(1)
