GenomeComb

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.

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

Conversion