Documentation

TableCodec

Reads tab deliminated tabular text files

Category ROD Codecs


Overview

  • Header: must begin with line HEADER or track (for IGV), followed by any number of column names, separated by whitespace.
  • Comment lines starting with # are ignored
  • Each non-header and non-comment line is split into parts by whitespace, and these parts are assigned as a map to their corresponding column name in the header. Note that the first element (corresponding to the HEADER column) must be a valid genome loc such as 1, 1:1 or 1:1-10, which is the position of the Table element on the genome. TableCodec requires that there be one value for each column in the header, and no more, on all lines.

File format example

     HEADER a b c
     1:1  1   2   3
     1:2  4   5   6
     1:3  7   8   9
 

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA