map

bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.

For example, one could use bedtools map to compute the average score of BEDGRAPH records that overlap genes. Since the fourth column in BEDGRAPH is the score, the following command illustrates how this would be done:

$ bedtools map -a genes.bed -b peaks.bedgraph -c 4 -o mean

Another example is discussed in this Biostars post.

Note

bedtools map requires each input file to be sorted by genome coordinate. For BED files, this can be done with sort -k1,1 -k2,2n. Other sorting criteria are allowed if a genome file (-g) is provides that specifies the expected chromosome order.

Note

The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference.

Usage and option summary

Usage:

bedtools map [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>

(or):

mapBed [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>

Option	Description
-c	Specify the column from the B file to map onto intervals in A. Default: 5
-o	Specify the operation that should be applied to -c. Valid operations: sum - numeric only count - numeric or text count_distinct - numeric or text min - numeric only max - numeric only absmin - numeric only absmax - numeric only mean - numeric only median - numeric only antimode - numeric or text collapse (i.e., print a comma separated list) - numeric or text distinct (i.e., print a comma separated list) - numeric or text concat (i.e., print a comma separated list) - numeric or text
-f	Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
-F	Minimum overlap required as a fraction of B. Default is 1E-9 (i.e., 1bp).
-r	Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
-e	Require that the minimum fraction be satisfied for A _OR_ B. In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied.
-s	Force “strandedness”. That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
-S	Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
-null	The value to print if no overlaps are found for an A interval. Default: "."
-header	Print the header from the A file prior to results.
-split	Treat “split” BAM (i.e., having an “N” CIGAR operation) or BED12 entries as distinct BED intervals. When using -sorted, memory usage remains low even for very large files.
-g	Specify a genome file the defines the expected chromosome order in the input files.

Default behavior - compute the sum of the score column for all overlaps.

By default, map computes the sum of the 5th column (the score field for BED format) for all intervals in B that overlap each interval in A.

Tip

Records in A that have no overlap will, by default, return . for the computed value from B. This can be changed with the -null option.

$ cat a.bed
chr1        10      20      a1      1       +
chr1        50      60      a2      2       -
chr1        80      90      a3      3       -

$ cat b.bed
chr1        12      14      b1      2       +
chr1        13      15      b2      5       -
chr1        16      18      b3      5       +
chr1        82      85      b4      2       -
chr1        85      87      b5      3       +

$ bedtools map -a a.bed -b b.bed
chr1        10      20      a1      1       +       12
chr1        50      60      a2      2       -       .
chr1        80      90      a3      3       -       5

mean Compute the mean of a column from overlapping intervals

$ cat a.bed
chr1        10      20      a1      1       +
chr1        50      60      a2      2       -
chr1        80      90      a3      3       -

$ cat b.bed
chr1        12      14      b1      2       +
chr1        13      15      b2      5       -
chr1        16      18      b3      5       +
chr1        82      85      b4      2       -
chr1        85      87      b5      3       +

$ bedtools map -a a.bed -b b.bed -c 5 -o mean
chr1        10      20      a1      1       +       4
chr1        50      60      a2      2       -       .
chr1        80      90      a3      3       -       2.5

collapse List each value of a column from overlapping intervals

$ bedtools map -a a.bed -b b.bed -c 5 -o collapse
chr1        10      20      a1      1       +       2,5,5
chr1        50      60      a2      2       -       .
chr1        80      90      a3      3       -       2,3

distinct List each unique value of a column from overlapping intervals

$ bedtools map -a a.bed -b b.bed -c 5 -o distinct
chr1        10      20      a1      1       +       2,5
chr1        50      60      a2      2       -       .
chr1        80      90      a3      3       -       2,3

-s Only include intervals that overlap on the same strand.

$ bedtools map -a a.bed -b b.bed -c 5 -o collapse -s
chr1        10      20      a1      1       +       2,5
chr1        50      60      a2      2       -       .
chr1        80      90      a3      3       -       2

-S Only include intervals that overlap on the opposite strand.

$ bedtools map -a a.bed -b b.bed -c 5 -o collapse -S
chr1        10      20      a1      1       +       5
chr1        50      60      a2      2       -       .
chr1        80      90      a3      3       -       3

Multiple operations and columns at the same time.

As of version 2.19.1, multiple columns and operations are allowed at the same time in a single run. This greatly expedites analyses by preventing one from having to process the same file over an over for each column/operation.

$ bedtools map -a a.bed -b b.bed -c 5,5,5,5 -o min,max,median,collapse

Or, apply the same function to multiple columns:

$ bedtools map -a a.bed -b b.bed -c 3,4,5,6 -o mean

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