1htsfile(1) Bioinformatics tools htsfile(1)
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6 htsfile - identify high-throughput sequencing data files
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9 htsfile [-chHv] FILE...
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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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55 bcftools(1), file(1), samtools(1)
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59htslib-1.9 18 July 2018 htsfile(1)