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Bedder Closest

The bedder closest command finds the nearest intervals between two BED files. Unlike intersect, which requires overlaps, closest can find the nearest intervals even when they don't overlap.

Basic Usage

Simple Closest

Find the closest intervals in target.bed for each interval in query.bed:

query.bed:

chr1 10 20
chr1 50 60

target.bed:

chr1 30 40
chr1 70 80

$ bedder closest -a query.bed -b target.bed -g genome.fai -n 1 -c distance
chr1 10 20 chr1 30 40 10
chr1 50 60 chr1 30 40 10

Each line shows:

  • The query interval (first 3 columns)
  • The closest target interval (next 3 columns)
  • The distance in bases (last column)

Distance

The distance column reports the number of bases between intervals:

  • 0 = overlapping intervals
  • Positive number = non-overlapping with that many bases between them
  • -1 = no intervals found within the specified constraints

Overlapping Intervals

When intervals overlap, the distance is 0:

single.bed:

chr1 25 35

$ bedder closest -a single.bed -b target.bed -g genome.fai -c distance
chr1 25 35 chr1 30 40 0

Finding Multiple Closest Intervals

Use -n or --n-closest to find multiple nearest intervals:

n-closest = 1 (default behavior with -n flag)

$ bedder closest -a multi.bed -b target.bed -g genome.fai -n 1 -c distance
chr1 5 10 chr1 30 40 20
chr1 25 35 chr1 30 40 0
chr1 45 50 chr1 30 40 5

n-closest = 2

Find the two closest intervals for each query:

$ bedder closest -a query.bed -b target.bed -g genome.fai -n 2 -c distance
chr1 10 20 chr1 30 40 chr1 70 80 10
chr1 50 60 chr1 30 40 chr1 70 80 10

Notice that each query interval now has two target intervals (6 columns for targets instead of 3).

Maximum Distance

Use -d or --max-distance to limit how far to search for closest intervals:

max-distance = 15

Only report intervals within 15 bases:

$ bedder closest -a query.bed -b target.bed -g genome.fai -d 15 -c distance
chr1 10 20 chr1 30 40 10
chr1 50 60 chr1 30 40 chr1 70 80 10

max-distance = 5

With a stricter limit, intervals beyond 5 bases are not reported (shown as -1):

$ bedder closest -a query.bed -b target.bed -g genome.fai -d 5 -c distance
chr1 10 20 -1
chr1 50 60 -1

The -1 indicates that no intervals were found within the specified maximum distance.

Default Behavior

Without -n or -d, bedder closest reports all overlapping intervals (similar to bedder intersect):

a.bed:

chr1 10 20
chr1 60 75

b.bed:

chr1 15 25
chr1 55 70

$ bedder closest -a a.bed -b b.bed -g genome.fai
chr1 10 20 chr1 15 25
chr1 60 75 chr1 55 70

Common Options

All standard bedder options work with closest:

  • -a <QUERY_PATH> - query file (required)
  • -b <OTHER_PATHS> - target file (required)
  • -g, --genome <GENOME_FILE> - genome file for chromosome ordering (required)
  • -c, --columns <COLUMNS> - additional columns to output (e.g., distance)
  • -o, --output <OUTPUT_PATH> - output file (default: stdout)
  • -n, --n-closest <N_CLOSEST> - report the n-closest intervals
  • -d, --max-distance <MAX_DISTANCE> - maximum distance to search
  • --python <PYTHON_FILE> - Python file with custom functions
  • -f, --filter <FILTER> - filter expression

Tips

  1. Use -c distance to see the actual distances between intervals
  2. Use -n 1 to find only the single closest interval for each query
  3. Use -d to limit searches and improve performance for large files
  4. Combine -n and -d to find the n-closest intervals within a maximum distance
  5. When neither -n nor -d is specified, closest behaves like intersect and only reports overlapping intervals