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1 .TH htsfile 1 "3 February 2015" "htslib-1.2.1" "Bioinformatics tools"
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2 .SH NAME
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3 htsfile \- identify high-throughput sequencing data files
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4 .\"
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5 .\" Copyright (C) 2015 Genome Research Ltd.
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6 .\"
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7 .\" Author: John Marshall <jm18@sanger.ac.uk>
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8 .\"
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9 .\" Permission is hereby granted, free of charge, to any person obtaining a
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10 .\" copy of this software and associated documentation files (the "Software"),
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11 .\" to deal in the Software without restriction, including without limitation
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12 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
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13 .\" and/or sell copies of the Software, and to permit persons to whom the
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14 .\" Software is furnished to do so, subject to the following conditions:
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15 .\"
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16 .\" The above copyright notice and this permission notice shall be included in
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17 .\" all copies or substantial portions of the Software.
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18 .\"
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19 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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20 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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21 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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22 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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23 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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24 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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25 .\" DEALINGS IN THE SOFTWARE.
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26 .\"
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27 .SH SYNOPSIS
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28 .B htsfile
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29 .RB [ -chH ]
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30 .IR FILE ...
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31 .SH DESCRIPTION
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32 The \fBhtsfile\fR utility attempts to identify what kind of high-throughput
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33 sequencing data files the specified files are, and provides minimal viewing
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34 capabilities for some kinds of data file.
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35 .P
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36 It can identify sequencing data files such as SAM, BAM, and CRAM;
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37 variant calling data files such as VCF and BCF;
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38 index files used to index these data files;
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39 and compressed versions of many of them.
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40 .P
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41 For each \fIFILE\fR given, \fBhtsfile\fP prints a description of the file
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42 format determined, using similar keyword conventions to \fBfile\fP(1):
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43 "text" indicates a textual file that can probably be viewed on a terminal;
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44 "data" indicates binary data;
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45 "sequence", "variant calling", and "index" indicate different categories of
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46 data file.
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47 When it can be identified, the name of the particular file format (such as
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48 "BAM" or "VCF") is printed at the start of the description.
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49 .P
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50 When used to view file contents as text, \fBhtsfile\fP can optionally show
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51 only headers or only data records, but has no other filtering capabilities.
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52 Use \fBsamtools\fR or \fBbcftools\fR if you need more extensive viewing or
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53 filtering capabilities.
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54 .P
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55 The following options are accepted:
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56 .TP 4n
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57 .BR -c ", " --view
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58 Instead of identifying the specified files, display a textual representation
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59 of their contents on standard output.
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60 .TP
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61 .BR -h ", " --header-only
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62 Display data file headers only.
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63 Implies \fB--view\fR.
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64 .TP
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65 .BR -H ", " --no-header
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66 When viewing files, display data records only.
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67 .PP
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68 .SH SEE ALSO
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69 .IR bcftools (1),
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70 .IR file (1),
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71 .IR samtools (1)
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