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 0.8.5
Most important changes in 0.8.5 are
Conversion
- support for version 2 Complete Genomics data
- var2annotvar updated to support version 2
- convert SV and CNV data (cg convcgsv and cg convcgcnv)
- added cg liftover (convert tsv files between different
builds, based on liftover)
- added cg exportplink
Annotation
- reference databases updated
- many updates on genes, ...
- info files also downloaded and added in defdb
- extra annotation files (1000glow, encode data)
Query
- cg_select extra options (-sh for separate header, -qf for
queryfile, -hf for headerfile) and functions (lmind and lmaxd)
- cg viz added: simple gui for viewing large tab separated
files
Validation
- genome_seq: extract sequence from regions of the genome (given
in regionfile), optinally masked for repeats and known snps
Tools
- cg razip, cg bgzip, cg unzip
- cg calcsequencedgenome
- cg cat
and many fixes
