Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

keyvalue

Format

cg keyvalue ?options? ?infile? ?outfile?

Summary

Converts data in tsv format from wide format (data for each sample in separate columns) to keyvalue format.

Description

Converts a tsv file containing different values of an object in one row (different fields) into a key-value format: Each of the rows is split into multiple rows (one for each data column) containing fields identifying the object followed by the fields key (fieldname of data column in original) \ and value (value in the data column).

The fields identifying the object can be specified using the -idfields option, but defaults to sample or id. sample as id field is treated special (unless an actual sample field is present in the file): The actual sample value is extracted from the fieldname (field-sample).

Arguments

infile: file to be converted, if not given, uses stdin. File may be compressed.
outfile: write results to outfile, if not given, uses stdout

Options

-idfields list: which fields identify the object (default sample or id)
-samplefields samplefields: Using this option, sample names that consist of several parts separated by - (as typical in genomecomb output, e.g. -gatk-rdsbwa-sample1) are split up in separate fields with the field names given by samplefields

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