GenomeComb

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Scientific applications

Filter Selection

Supplementary Data Reumers, De Rijk et al

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)

cg2tsv

Format

cg cg2tsv ?options? cgvarfile ?cggenefile? outputfile

Summary

Converts data in Complete Genomics format to tsv (tab separated, simple feature table) format. The command will also sort the tsv appropriately. The cggenefile is optional. It contains the CG gene annotations, which can be (best) left out as these annotations (and more) can be done in genomecomb.

Arguments

cgvarfile

Complete genomics var file to be converted. File may be compressed.

cggenefile

Complete genomics gene file to be converted.

outfile

write results to outfile

Options

-split

if 1, multiple alternative alleles will be on a separate lines, treated mostly as a separate variant

-sorted 0/1

Use 1 if the CG var and gene file are already sorted (so they are not sorted gain first)

-ref refname

name of reference genome that will be put in the comment of the tsv file, e.g. hg19. If not given it will detect hg18 or hg19 from the comments in the CG file

Category

Format Conversion