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)
Makesequenom
Format
cg makesequenom ?options? targetsfile resultfile dbdir
Summary
Make input files for designing sequenom validation experiments
Description
This command makes an input file that can be used for sequenom
assay design for the variants in targetsfile. Targetsfile is a tab
delimited file with at least following columns: chromosome begin end
ref alt
Arguments
- targetsfile
- tab delimited file containing targets with at least following
columns: chromosome begin end ref alt
- resultfile
- sequenom assay setup results
- dbdir
- directory containing reference genomes and variation data
Options
- -f freq
- only softmask (lowercase) dbsnp variants if they have a
frequency > freq (default is 0, use -1 to include all)
- -n freq
- only mask (using N) dbsnp variants if they have a frequency
> freq (default is 0.2, use -1 to include all)
- -p snpdbpattern
- determines which variant databases are used
(dbdir/var_*snpdbpattern*.tsv.gz). default is "snp" for
dbsnp. you can e.g. use "Common" for the common variants
in dbsnp
- -d delsize
- only mask (using N) dbsnp variants if they are smaller than
delsize (default is 5, use -1 to include all)
- -r 0/s/N
- if 0, repeatmasker repeats are not masked, N will hardmask
(replace by N) them. Default is to softmask (s).
Category
Validation
