1htsfile(1)                   Bioinformatics tools                   htsfile(1)
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NAME

6       htsfile - identify high-throughput sequencing data files
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SYNOPSIS

9       htsfile [-chHv] FILE...
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DESCRIPTION

12       The  htsfile  utility attempts to identify what kind of high-throughput
13       sequencing data files the specified files  are,  and  provides  minimal
14       viewing capabilities for some kinds of data file.
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16       It can identify sequencing data files such as SAM, BAM, and CRAM; vari‐
17       ant calling data files such as VCF and BCF; index files used  to  index
18       these data files; and compressed versions of many of them.
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20       For  each  FILE  given, htsfile prints a description of the file format
21       determined, using similar keyword conventions to file(1): "text"  indi‐
22       cates  a textual file that can probably be viewed on a terminal; "data"
23       indicates binary data; "sequence", "variant calling", and "index" indi‐
24       cate different categories of data file.  When it can be identified, the
25       name of the particular file format (such as "BAM" or "VCF") is  printed
26       at the start of the description.
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28       When  used  to  view file contents as text, htsfile can optionally show
29       only headers or only data records, but has no other filtering capabili‐
30       ties.   Use  samtools or bcftools if you need more extensive viewing or
31       filtering capabilities.
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33       The following options are accepted:
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35       -c, --view
36           Instead of identifying the specified files, display a textual  rep‐
37           resentation of their contents on standard output.
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39           By  default,  --view  refuses  to display files in unknown formats.
40           When --verbose is also given, the raw contents of  such  files  are
41           displayed,  with  non-printable  characters  shown via C-style "\x"
42           hexadecimal escape sequences.
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44       -h, --header-only
45           Display data file headers only.  Implies --view.
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47       -H, --no-header
48           When viewing files, display data records only.
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50       -v, --verbose
51           Display additional warnings and diagnostic messages.  Using  --ver‐
52           bose repeatedly further raises the verbosity.
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SEE ALSO

55       bcftools(1), file(1), samtools(1)
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59htslib-1.9                       18 July 2018                       htsfile(1)
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