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SV Incorporation

Step 3 -- incorporating SVs into patient table

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.

Usage

Default

Default options can be found

What `SV_incorporation.R` does

1. Only SVs implicating any ACCESS SV calling key genes are retained
to similar format to ACCESS SV output

SV Incorporation

Step 3 -- incorporating SVs into patient table

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.

Usage

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

Default options can be found

What `SV_incorporation.R` does

1. Only SVs implicating any ACCESS SV calling key genes are retained
to similar format to ACCESS SV output

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]

SV Incorporation

hashtagUsage

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hashtagWhat SV_incorporation.R does

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SV Incorporation

hashtagUsage

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hashtagWhat SV_incorporation.R does

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Usage

Default

What `SV_incorporation.R` does

Usage

Default

What `SV_incorporation.R` does