.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH BEDMAP "1" "March 2024" "bedmap 2.4.41+dfsg" "User Commands"
.SH NAME
bedmap \- manual page for bedmap 2.4.41+dfsg
.SH DESCRIPTION
bedmap
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citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
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https://doi.org/10.1093/bioinformatics/bts277
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version:
2.4.41 (typical)
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authors:
Shane Neph & Scott Kuehn
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USAGE: bedmap [process\-flags] [overlap\-option] <operation(s)...> <ref\-file> [map\-file]
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Any input file must be sorted per the sort\-bed utility.
The program accepts BED and Starch file formats.
You may use '\-' for a BED file to indicate the input comes from stdin.
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Traverse <ref\-file>, while applying <operation(s)> on qualified, overlapping elements from
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<map\-file>.
Output is one line for each line in <ref\-file>, sent to standard output.  There
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is no limit on the number of operations you can specify to compute in one bedmap call.
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If <map\-file> is omitted, the given file is treated as both the <ref\-file> and <map\-file>.
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This usage is more efficient than specifying the same file twice.
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Arguments may be given in any order before the input file(s).
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Process Flags:
.HP
\fB\-\-\-\-\-\-\-\-\fR
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\fB\-\-chrom\fR <chromosome>
Jump to and process data for given <chromosome> only.
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\fB\-\-delim\fR <delim>
Change output delimiter from '|' to <delim> between columns (e.g. '\et').
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\fB\-\-ec\fR
Error check all input files (slower).
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\fB\-\-faster\fR
(advanced) Strong input assumptions are made.  Compatible with:
\fB\-\-bp\-ovr\fR, \fB\-\-range\fR, \fB\-\-fraction\-both\fR, and \fB\-\-exact\fR overlap options only.
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\fB\-\-header\fR
Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
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\fB\-\-help\fR
Print this message and exit successfully.
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\fB\-\-min\-memory\fR
Minimize memory usage (slower).
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\fB\-\-multidelim\fR <delim>
Change delimiter of multi\-value output columns from ';' to <delim>.
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\fB\-\-prec\fR <int>
Change the post\-decimal precision of scores to <int>.  0 <= <int>.
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\fB\-\-sci\fR
Use scientific notation for score outputs.
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\fB\-\-skip\-unmapped\fR
Print no output for a row with no mapped elements.
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\fB\-\-sweep\-all\fR
Ensure <map\-file> is read completely (helps to prevent broken pipes).
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\fB\-\-unmapped\-val\fR <val>
Print <val> on unmapped \fB\-\-echo\-map\fR* and \fB\-\-min\fR/max\-element* operations.
The default is to print nothing.
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\fB\-\-version\fR
Print program information.
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Overlap Options (At most, one may be selected.
By default, \fB\-\-bp\-ovr\fR 1 is used):
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\fB\-\-\-\-\-\-\-\-\fR
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\fB\-\-bp\-ovr\fR <int>
Require <int> bp overlap between elements of input files.
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\fB\-\-exact\fR
First 3 fields from <map\-file> must be identical to <ref\-file>'s.
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\fB\-\-fraction\-both\fR <val>
Both \fB\-\-fraction\-ref\fR <val> and \fB\-\-fraction\-map\fR <val> must be true to
qualify as overlapping.  Expect 0 < val <= 1.
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\fB\-\-fraction\-either\fR <val>
Either \fB\-\-fraction\-ref\fR <val> or \fB\-\-fraction\-map\fR <val> must be true to
qualify as overlapping.  Expect 0 < val <= 1.
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\fB\-\-fraction\-map\fR <val>
The fraction of the element's size from <map\-file> that must overlap
the element in <ref\-file>.  Expect 0 < val <= 1.
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\fB\-\-fraction\-ref\fR <val>
The fraction of the element's size from <ref\-file> that must overlap
an element in <map\-file>.  Expect 0 < val <= 1.
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\fB\-\-range\fR <int>
Grab <map\-file> elements within <int> bp of <ref\-file>'s element,
where 0 <= int.  \fB\-\-range\fR 0 is an alias for \fB\-\-bp\-ovr\fR 1.
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Operations:
(Any number of operations may be used any number of times.)
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\fB\-\-\-\-\-\-\-\-\-\-\fR
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SCORE:
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<ref\-file> must have at least 3 columns and <map\-file> 5 columns.
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\fB\-\-cv\fR
The result of \fB\-\-stdev\fR divided by the result of \fB\-\-mean\fR.
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\fB\-\-kth\fR <val>
Generalized median. Report the value, x, such that the fraction <val>
of overlapping elements' scores from <map\-file> is less than x,
and the fraction 1\-<val> of scores is greater than x.  0 < val <= 1.
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\fB\-\-mad\fR <mult=1>
The median absolute deviation of overlapping elements in <map\-file>.
Multiply mad score by <mult>.  0 < mult, and mult is 1 by default.
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\fB\-\-max\fR
The highest score from overlapping elements in <map\-file>.
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\fB\-\-max\-element\fR
A (non\-random) highest\-scoring and overlapping element in <map\-file>.
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\fB\-\-max\-element\-rand\fR
A random highest\-scoring and overlapping element in <map\-file>.
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\fB\-\-mean\fR
The average score from overlapping elements in <map\-file>.
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\fB\-\-median\fR
The median score from overlapping elements in <map\-file>.
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\fB\-\-min\fR
The lowest score from overlapping elements in <map\-file>.
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\fB\-\-min\-element\fR
A (non\-random) lowest\-scoring and overlapping element in <map\-file>.
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\fB\-\-min\-element\-rand\fR
A random lowest\-scoring and overlapping element in <map\-file>.
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\fB\-\-stdev\fR
The square root of the result of \fB\-\-variance\fR.
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\fB\-\-sum\fR
Accumulated scores from overlapping elements in <map\-file>.
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\fB\-\-tmean\fR <low> <hi>
The mean score from overlapping elements in <map\-file>, after
ignoring the bottom <low> and top <hi> fractions of those scores.
0 <= low <= 1.  0 <= hi <= 1.  low+hi <= 1.
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\fB\-\-variance\fR
The variance of scores from overlapping elements in <map\-file>.
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\fB\-\-wmean\fR
Weighted mean, scaled in proportion to the coverage of the <ref\-file>
element by each overlapping <map\-file> element.
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\fB\-\-\-\-\-\-\-\-\-\-\fR
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NON\-SCORE:
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<ref\-file> must have at least 3 columns.
For \fB\-\-echo\-map\-id\fR/echo\-map\-id\-uniq, <map\-file> must have at least 4 columns.
For \fB\-\-echo\-map\-score\fR, <map\-file> must have at least 5 columns.
For all others, <map\-file> requires at least 3 columns.
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\fB\-\-bases\fR
The total number of overlapping bases from <map\-file>.
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\fB\-\-bases\-uniq\fR
The number of distinct bases from <ref\-file>'s element covered by
overlapping elements in <map\-file>.
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\fB\-\-bases\-uniq\-f\fR
The fraction of distinct bases from <ref\-file>'s element covered by
overlapping elements in <map\-file>.
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\fB\-\-count\fR
The number of overlapping elements in <map\-file>.
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\fB\-\-echo\fR
Print each line from <ref\-file>.
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\fB\-\-echo\-map\fR
List all overlapping elements from <map\-file>.
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\fB\-\-echo\-map\-id\fR
List IDs from all overlapping <map\-file> elements.
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\fB\-\-echo\-map\-id\-uniq\fR
List unique IDs from overlapping <map\-file> elements.
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\fB\-\-echo\-map\-range\fR
Print genomic range of overlapping elements from <map\-file>.
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\fB\-\-echo\-map\-score\fR
List scores from overlapping <map\-file> elements.
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\fB\-\-echo\-map\-size\fR
List the full length of every overlapping element.
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\fB\-\-echo\-overlap\-size\fR List lengths of overlaps.
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\fB\-\-echo\-ref\-name\fR
Print the first 3 fields of <ref\-file> using chrom:start\-end format.
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\fB\-\-echo\-ref\-row\-id\fR
Print 'id\-' followed by the line number of <ref\-file>.
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\fB\-\-echo\-ref\-size\fR
Print the length of each line from <ref\-file>.
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\fB\-\-indicator\fR
Print 1 if there exists an overlapping element in <map\-file>, 0 otherwise.
.SH "SEE ALSO"
The full documentation for
.B bedmap
is maintained as a Texinfo manual.  If the
.B info
and
.B bedmap
programs are properly installed at your site, the command
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.B info bedmap
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should give you access to the complete manual.