.. _merge: ############### *merge* ############### | .. image:: ../images/tool-glyphs/merge-glyph.png :width: 600pt | ``bedtools merge`` combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features. .. note:: ``bedtools merge`` requires that you presort your data by chromosome and then by start position (e.g., ``sort -k1,1 -k2,2n in.bed > in.sorted.bed`` for BED files). .. seealso:: :doc:`../tools/cluster` :doc:`../tools/complement` ========================================================================== Usage and option summary ========================================================================== **Usage**: :: bedtools merge [OPTIONS] -i **(or)**: :: mergeBed [OPTIONS] -i =========================== =============================================================================================================================================================================================================== Option Description =========================== =============================================================================================================================================================================================================== **-s** Force strandedness. That is, only merge features that are the same strand. *By default, this is disabled*. **-S** Force merge for one specific strand only. Follow with + or - to force merge from only the forward or reverse strand, respectively. *By default, merging is done without respect to strand*. **-d** Maximum distance between features allowed for features to be merged. *Default is 0. That is, overlapping and/or book-ended features are merged*. **-c** Specify columns from the input file to operate upon (see -o option, below). Multiple columns can be specified in a comma-delimited list. **-o** | Specify the operation that should be applied to ``-c``. | Valid operations: | sum, min, max, absmin, absmax, | mean, median, | collapse (i.e., print a delimited list (duplicates allowed)), | distinct (i.e., print a delimited list (NO duplicates allowed)), | count | count_distinct (i.e., a count of the unique values in the column), | **Default:** sum | Multiple operations can be specified in a comma-delimited list. | If there is only column, but multiple operations, all operations will be | applied on that column. Likewise, if there is only one operation, but | multiple columns, that operation will be applied to all columns. | Otherwise, the number of columns must match the the number of operations, | and will be applied in respective order. | | E.g., ``-c 5,4,6 -o sum,mean,count`` will give the sum of column 5, | the mean of column 4, and the count of column 6. | The order of output columns will match the ordering given in the command. **-header** | Print the header from the A file prior to results. **-delim** | Specify a custom delimiter for the -nms and -scores concat options | Example: ``-delim "|"`` | ``Default: ";"`` =========================== =============================================================================================================================================================================================================== ========================================================================== Default behavior ========================================================================== By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or bookended intervals into a single, "flattened" or "merged" interval. .. code-block:: bash $ cat A.bed chr1 100 200 chr1 180 250 chr1 250 500 chr1 501 1000 $ bedtools merge -i A.bed chr1 100 500 chr1 501 1000 ========================================================================== ``-s`` Enforcing "strandedness" ========================================================================== The ``-s`` option will only merge intervals that are overlapping/bookended *and* are on the same strand. .. code-block:: bash $ cat A.bed chr1 100 200 a1 1 + chr1 180 250 a2 2 + chr1 250 500 a3 3 - chr1 501 1000 a4 4 + $ bedtools merge -i A.bed -s chr1 100 250 chr1 501 1000 chr1 250 500 To also report the strand, you could use the ``-c`` and ``-o`` operators (see below for more details): .. code-block:: bash $ bedtools merge -i A.bed -s -c 6 -o distinct chr1 100 250 + chr1 501 1000 + ========================================================================== ``-S`` Reporting merged intervals on a specific strand. ========================================================================== The ``-S`` option will only merge intervals for a specific strand. For example, to only report merged intervals on the "+" strand: .. code-block:: bash $ cat A.bed chr1 100 200 a1 1 + chr1 180 250 a2 2 + chr1 250 500 a3 3 - chr1 501 1000 a4 4 + $ bedtools merge -i A.bed -S + chr1 100 250 chr1 501 1000 To also report the strand, you could use the ``-c`` and ``-o`` operators (see below for more details): .. code-block:: bash $ bedtools merge -i A.bed -S + -c 6 -o distinct chr1 100 250 + chr1 501 1000 + ========================================================================== ``-d`` Controlling how close two features must be in order to merge ========================================================================== By default, only overlapping or book-ended features are combined into a new feature. However, one can force ``merge`` to combine more distant features with the ``-d`` option. For example, were one to set ``-d`` to 1000, any features that overlap or are within 1000 base pairs of one another will be combined. .. code-block:: bash $ cat A.bed chr1 100 200 chr1 501 1000 $ bedtools merge -i A.bed chr1 100 200 chr1 501 1000 $ bedtools merge -i A.bed -d 1000 chr1 100 200 1000 ========================================================================== ``-c`` and ``-o`` Applying operations to columns from merged intervals. ========================================================================== When merging intervals, we often want to summarize or keep track of the values observed in specific columns (e.g., the feature name or score) from the original, unmerged intervals. When used together, the ``-c`` and ``-o`` options allow one to select specific columns (``-c``) and apply operation (``-o``) to each column. The result will be appended to the default, merged interval output. For example, one could use the following to report the count of intervals that we merged in each resulting interval (this replaces the ``-n`` option that existed prior to version ``2.20.0``). .. code-block:: bash $ cat A.bed chr1 100 200 chr1 180 250 chr1 250 500 chr1 501 1000 $ bedtools merge -i A.bed -c 1 -o count chr1 100 500 3 chr1 501 1000 1 We could also use these options to report the mean of the score (#5) field: .. code-block:: bash $ cat A.bed chr1 100 200 a1 1 + chr1 180 250 a2 2 + chr1 250 500 a3 3 - chr1 501 1000 a4 4 + $ bedtools merge -i A.bed -c 5 -o mean chr1 100 500 2 chr1 501 1000 4 Let's get fancy and report the mean, min, and max of the score column: .. code-block:: bash $ bedtools merge -i A.bed -c 5 -o mean,min,max chr1 100 500 2 1 3 chr1 501 1000 4 4 4 Let's also report a comma-separated list of the strands: .. code-block:: bash $ bedtools merge -i A.bed -c 5,5,5,6 -o mean,min,max,collapse chr1 100 500 2 1 3 +,+,- chr1 501 1000 4 4 4 + Hopefully this provides a clear picture of what can be done. ========================================================================== ``-n`` Reporting the number of features that were merged ========================================================================== .. deprecated:: 2.20.0 See the ``-c`` and ``-o`` operators. ========================================================================== ``-nms`` Reporting the names of the features that were merged ========================================================================== .. deprecated:: 2.20.0 See the ``-c`` and ``-o`` operators. ========================================================================== ``-scores`` Reporting the scores of the features that were merged ========================================================================== .. deprecated:: 2.20.0 See the ``-c`` and ``-o`` operators. ========================================================================== ``-delim`` Change the delimiter for ``-c`` and ``-o`` ========================================================================== One can override the use of a comma as the delimiter for the ``-c`` and ``-o collapse|distinct`` options via the use of the ``-delim`` option. .. code-block:: bash $ cat A.bed chr1 100 200 A1 chr1 150 300 A2 chr1 250 500 A3 Compare: .. code-block:: bash $ bedtools merge -i A.bed -c 4 -o collapse chr1 100 500 A1,A2,A3 to: .. code-block:: bash $ bedtools merge -i A.bed -c 4 -o collapse -delim "|" chr1 100 500 A1|A2|A3