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wide

Format

cg wide ?options? ?infile? ?outfile?

Summary

Converts data in tsv format from long format (data for each sample in separate lines) to wide format (data for each sample in separate columns)

Description

Genomecomb usually expects data in tsv files in wide format, where some fields are common/general for all samples (e.g. chromosome, begin, end, .. for variants) and some fields have specific values for each sample (e.g. quality, coverage, ...). In wide format these columns are named by adding "-samplename" to the fieldname. In the long format, sample specific data is on separate lines (the common fields are repeated in each line). "cg wide" converts from long to wide format. "cg long" can be used for the reverse.

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

-f commonfields (--fields)

set which fields will be used as common fields. Wildcards may be used in defining the fielnames. (default is the variant fields chromosome, begin, ... present in the file).

-s samplefields (--samplefields)

set which fields will be used as fields to define the sample. Wildcards may be used in defining the fielnames. (default is all of sample,sample1,sample2,sample3,mapping,varcall present in the file).

Category

Format Conversion