GenomeComb

clc2sft

Format

cg clc2sft ?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

Conversion