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)
releasenotes 0.11.0
Release 0.11.0
Several improvements have been made, some highlights:
HOMWES
cg homwes and cg homwes_compare can be used to do homozygosity
mapping (using filtering and PLINK) on whole exome data
Important improvements in liftover
- cg liftover is completely rewritten to properly lift variants,
by correcting for changes in the reference sequence and in
strandness. (it no longer uses UCSC liftOver)
- added cg liftregion and liftsample
- cg liftfindchanges, liftchain2tsv
genelist based annotation support
- cg geneannot2reg can be used to create a (region) annotation
file based on a gene (names) list with annotations and a gene
region file (e.g. hg19/extra/reg_hg19_genes.tsv)
- support for downloading several interesting genelists:
- cg downloaddb phenotype: uses biomart (ensembl geneset) and
clinvar for finding gene-phenotype correlations
- cg downloadmart: can be used to download gene ontology
data
- cg downloadbiograph: download ranking of genes vs a
disease from biograph
new and updated anotation databases
- directory with optional extra annotations (extra): go (gene
ontology), evs, ...
- phenotype
- 1000g3: phase 3 of 1000genomes project
- dbsnp142
- ...
new and improved commands
- cg cat: added -fields option
- cg select: added functions toupper, regsub
- cg lz4: alternative (fast) compression
