Prepare samples

Sort data, Convert variations and gene annotation information to one annotated variation file called

cg process_sample originalsampledir sampledir dbdir ?force?

Important files in the resulting sample dir are:

cg process_rtgsample originalsampledir sampledir ?force?

does similar for RTG data. It expects two subdirs in originalsampledir:

Compare genomes

Compare samples by making a file containing information of all samples in a wide table (tab separated), where each line contains general variant info (position, type, annotation, etc.), plus columns with variant info specific to each sample (genotype, coverage, etc.). The latter have a column heading of the form info-samplename

mkdir resultsdir
cg multicompar resultsdir/mcomparfile sampledir ... ...

Complete annotation info in multicompar file: Information that is not directly in the individual variant files, such as coverage for a sample where the variant was not called, is extracted from the full data files, and added to the multicompar file.

cg multicompar_reannot resultsdir/mcomparfile

Annotate comparison file

Add (a lot of) annotations to the mcomparfile using:

cg annotate mcomparfile resultfile dbdir

Select variants

cg select can be used to easily query the resulting file.

cg select ?options? ?infile? ?outfile?

More info can be found in the help on select