Provided by: bedops_2.4.35+dfsg-1_amd64 bug

NAME

       bedmap - manual page for bedmap 2.4.35+dfsg

DESCRIPTION

       bedmap

              citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract

              https://doi.org/10.1093/bioinformatics/bts277

       version:
              2.4.35 (typical)

       authors:
              Shane Neph & Scott Kuehn

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

              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.

              Traverse  <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).

              Process Flags:

       --------

       --chrom <chromosome>
              Jump to and process data for given <chromosome> only.

       --delim <delim>
              Change output delimiter from '|' to <delim> between columns (e.g. '\t').

       --ec   Error check all input files (slower).

       --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.

       --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).

       --version
              Print program information.

       Overlap Options (At most, one may be selected.
              By default, --bp-ovr 1 is used):

       --------

       --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.)

       ----------

              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:

              <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.