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)
clc2tsv
Format
cg clc2tsv ?options? ?infile? ?outfile?
Summary
Converts output from the clc bio assembly cell snp caller to sft
(simple feature table) format
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
- -coverage coverage
- variants at position with coverage below this value will be
considered unsequenced: variant data is present in output, but the
"sequenced" column gets value "u" (default: 0)
- -minfreq cutoff
- Position with a frequency >= cutoff (default: 0.25)
will be considered variant: the "sequenced" column gets
value "v"; if lower "sequenced" will be
"r"
Category
Format Conversion
