The third step takes all the SV variants from all samples within each patient and present them in the same format as SNVs and incorporate SVs in the patient level table.
Rscript R/SV_incorporation.R -h
usage: R/SV_incorporation.R [-h] [-m MASTERREF] [-o RESULTSDIR] [-dmp DMPDIR]
[-c CRITERIA]
optional arguments:
-h, --help show this help message and exit
-m MASTERREF, --masterref MASTERREF
File path to master reference file
-o RESULTSDIR, --resultsdir RESULTSDIR
Output directory
-dmp DMPDIR, --dmpdir DMPDIR
Directory of clinical DMP IMPACT repository [default]
-genes GENELIST, --genelist GENELIST
File path to genes covered by ACCESS [default]
-c CRITERIA, --criteria CRITERIA
Calling criteria [default]
Default options can be found here
SV_incorporation.R
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