bedmap - manual page for bedmap 2.4.41+dfsg
bedmap
- citation:
http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
- https://doi.org/10.1093/bioinformatics/bts277
- version:
- 2.4.41 (typical)
- 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.
- Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
- --help
- Print this message and exit successfully.
- --min-memory
- Minimize memory usage (slower).
- --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).
- --unmapped-val
<val>
- Print <val> on unmapped --echo-map* and
--min/max-element* operations. The default is to print
nothing.
- --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.
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.