BEDMAP(1)

📦
version 2.4.42 · 5 versions
, in ubuntu resolute, ubuntu stonking

🌸 bedmap(1) — the manual page for bedmap 🌸

okay bestie, sit down, hydrate, and let me tell you about bedmap — it's a User Command, it lives in section 1 of the manual, and this is the manual page for bedmap 2.4.42+dfsg. 💖

✨ NAME ✨

bedmap — manual page for bedmap 2.4.42+dfsg. That's it, that's the name, short and iconic. 👑

🦋 DESCRIPTION 🦋

bedmap 💅

citation:

version: 2.4.42 (typical)

authors: Shane Neph & Scott Kuehn 🫶 (yes, two whole authors, we love a collab)

USAGE: bedmap [process-flags] [overlap-option] <operation(s)...>
<ref-file> [map-file]

So here's the tea ☕ — 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. 🎀

It traverses <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). Slay, flexible queen. 💅

🎀 Process Flags 🎀

bestie this is the whole list, no skipping, we're eating the whole plate 🍓
  • --chrom <chromosome> — Jump to and process data for given <chromosome> only. One chromosome, main character energy. 👑
  • --delim <delim> — Change output delimiter from '|' to <delim> between columns (e.g. '\t').
  • --ec — Error check all input files (slower). Thorough but it's giving... slow. 😭
  • --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. nerd mode activated 🧚
  • --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. One. Pick one. This is not a build-your-own-sundae situation. 🍓
  • --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.) Go off, bestie, stack 'em. 💅

🔥 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 🦋

Here's the column tea, bestie: <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. 📖✨

okay that's the whole thing, you ate that, go forth and map your beds 💅

sign-off: this was bedmap 2.4.42+dfsg, dated August 2025, section BEDMAP(1) — mwah, ily, bye 🫶🌸

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