---
name: "bedmap"
section: "1"
platform: "linux"
package: "bedops"
version: "2.4.41+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bedmap"
---

# bedmap(1)

manual page for bedmap 2.4.41+dfsg

## NAME

bedmap - manual page for bedmap 2.4.41+dfsg

## DESCRIPTION

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.

- **--header**

  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.

## 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.