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)
multicompar
Prepare samples
Sort data, Convert variations and gene annotation information to
one annotated variation file called
- one variation (2 alleles) per line
- including gene information for the variations that have it It
also creates
- region files such as the ref-(in)consistent regions and
clusters of variations are located
- some (genome) coverage data
cg process_sample originalsampledir sampledir dbdir ?force?
- originalsampledir: is a directory with the sample data as it
comes from from CG, nothing will be changed in this dir
- sampledir: a directory with the sample data in genomecombs
formats, that will be created if not present yet; if present, files
not created yet will be added (e.g. after stopped job)
- dbdir: directory containing reference databases
- ?force?: if the parameter force is given, the command will
restart from the beginning, and redo every step. If not given, the
command will only create files that do not exist yet.
Important files in the resulting sample dir are:
- fannotvar-samplename.tsv: file containing the variant list with
annotations in tab separated format
- sreg-samplename.tsv: region file with the regions that are
considered as sequenced by CG
- coverage: directory containing files with genomewide coverage
(per chromosme) Other informative files in the resulting sample dir
are:
- reg_cluster.tsv: region file containing regions with
clustered variants
- reg_lowscore.tsv: region file containing regions with low
variant score
- reg_nocall.tsv: region file containing regions that contain
at least one nocall allele
- reg_refcons.tsv: region file containing regions that contain
at least one allele score as refconsistant / refinconsistent
(uncertain)
cg process_rtgsample originalsampledir sampledir ?force?
does similar for RTG data. It expects two subdirs in
originalsampledir:
- ori: dir containing original rtg variation file (pattern
*unfiltered.snp*)
- allpos: dir with files with info on full genome (pattern
chr${chr}_snps.txt) The resulting sampledir is similar to the one
produced by process_sample (not all files are present)
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 ... ...
- sampledir: processed (using process_sample) sample directories
to be compared
- resultsdir/mcomparfile: The sampledirs given will be added to
this file. The sampledirs are expected to be one dir below the
resultdir.
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
- resultsdir/mcomparfile: The sampledirs given will be added to
this file. The sampledirs are expected to be one dir below the
resultdir.
Annotate comparison file
Add (a lot of) annotations to the mcomparfile using:
cg annotate mcomparfile resultfile dbdir
- mcomparfile: variant file (can be from multicomparison, has to
have alt field)
- resultfile: new file that will be written: mcomparfile+ added
columns with annotation
- dbdir: directory containing reference databases and
annotation files (.../hg18)
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
