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 (default), 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