Category
Genomic Interval Manipulation
Usage
mergeBed [OPTIONS] -i
Manual
-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: ";"
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