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bedmap - manual page for bedmap 2.4.26+dfsg

BEDMAP(1) User Commands BEDMAP(1)

NAME

bedmap - manual page for bedmap 2.4.26+dfsg

DESCRIPTION

bedmap
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract version: 2.4.26 authors: Shane Neph & Scott Kuehn
USAGE: bedmap [process-flags] [overlap-option] <operation(s)...> <ref-file> [map-file]
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.
Traverse <ref-file>, while applying <operation(s)> on qualified, overlapping elements from
<map-file>.
Output is one line for each line in <ref-file>, sent to standard output. There
is no limit on the number of operations you can specify to compute in one bedmap call.
If <map-file> is omitted, the given file is treated as both the <ref-file> and <map-file>.
This usage is more efficient than specifying the same file twice.
Arguments may be given in any order before the input file(s).
Process Flags:
--------
--chrom <chromosome>
Jump to and process data for given <chromosome> only.
--delim <delim>
Change output delimiter from '|' to <delim> between columns (e.g. '\t').
--ec
Error check all input files (slower).
--faster
(advanced) Strong input assumptions are made. Compatible with: --bp-ovr, --range, --fraction-both, and --exact overlap options only.
--header
Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
--help
Print this message and exit successfully.
--multidelim <delim>
Change delimiter of multi-value output columns from ';' to <delim>.
--prec <int>
Change the post-decimal precision of scores to <int>. 0 <= <int>.
--sci
Use scientific notation for score outputs.
--skip-unmapped
Print no output for a row with no mapped elements.
--sweep-all
Ensure <map-file> is read completely (helps to prevent broken pipes).
--version
Print program information.
Overlap Options (At most, one may be selected.
By default, --bp-ovr 1 is used):
--------
--bp-ovr <int>
Require <int> bp overlap between elements of input files.
--exact
First 3 fields from <map-file> must be identical to <ref-file>'s.
--fraction-both <val>
Both --fraction-ref <val> and --fraction-map <val> must be true to qualify as overlapping. Expect 0 < val <= 1.
--fraction-either <val>
Either --fraction-ref <val> or --fraction-map <val> must be true to qualify as overlapping. Expect 0 < val <= 1.
--fraction-map <val>
The fraction of the element's size from <map-file> that must overlap the element in <ref-file>. Expect 0 < val <= 1.
--fraction-ref <val>
The fraction of the element's size from <ref-file> that must overlap an element in <map-file>. Expect 0 < val <= 1.
--range <int>
Grab <map-file> elements within <int> bp of <ref-file>'s element, where 0 <= int. --range 0 is an alias for --bp-ovr 1.
Operations:
(Any number of operations may be used any number of times.)
----------
SCORE:
<ref-file> must have at least 3 columns and <map-file> 5 columns.
--cv
The result of --stdev divided by the result of --mean.
--kth <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.
--mad <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.
--max
The highest score from overlapping elements in <map-file>.
--max-element
A (non-random) highest-scoring and overlapping element in <map-file>.
--max-element-rand
A random highest-scoring and overlapping element in <map-file>.
--mean
The average score from overlapping elements in <map-file>.
--median
The median score from overlapping elements in <map-file>.
--min
The lowest score from overlapping elements in <map-file>.
--min-element
A (non-random) lowest-scoring and overlapping element in <map-file>.
--min-element-rand
A random lowest-scoring and overlapping element in <map-file>.
--stdev
The square root of the result of --variance.
--sum
Accumulated scores from overlapping elements in <map-file>.
--tmean <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.
--variance
The variance of scores from overlapping elements in <map-file>.
--wmean
Weighted mean, scaled in proportion to the coverage of the <ref-file> element by each overlapping <map-file> element.
----------
NON-SCORE:
<ref-file> must have at least 3 columns. For --echo-map-id/echo-map-id-uniq, <map-file> must have at least 4 columns. For --echo-map-score, <map-file> must have at least 5 columns. For all others, <map-file> requires at least 3 columns.
--bases
The total number of overlapping bases from <map-file>.
--bases-uniq
The number of distinct bases from <ref-file>'s element covered by overlapping elements in <map-file>.
--bases-uniq-f
The fraction of distinct bases from <ref-file>'s element covered by overlapping elements in <map-file>.
--count
The number of overlapping elements in <map-file>.
--echo
Print each line from <ref-file>.
--echo-map
List all overlapping elements from <map-file>.
--echo-map-id
List IDs from all overlapping <map-file> elements.
--echo-map-id-uniq
List unique IDs from overlapping <map-file> elements.
--echo-map-range
Print genomic range of overlapping elements from <map-file>.
--echo-map-score
List scores from overlapping <map-file> elements.
--echo-map-size
List the full length of every overlapping element.
--echo-overlap-size List lengths of overlaps.
--echo-ref-name
Print the first 3 fields of <ref-file> using chrom:start-end format.
--echo-ref-row-id
Print 'id-' followed by the line number of <ref-file>.
--echo-ref-size
Print the length of each line from <ref-file>.
--indicator
Print 1 if there exists an overlapping element in <map-file>, 0 otherwise.

SEE ALSO

The full documentation for bedmap is maintained as a Texinfo manual. If the info and bedmap programs are properly installed at your site, the command
info bedmap
should give you access to the complete manual.
June 2017 bedmap 2.4.26+dfsg