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Filter Calls

Step 2 -- filtering

The second step takes all the genotypes generated from the first step and organized into a patient level variants table with VAFs and call status for each variant of each sample.

Each call is subjected to:

Read depth filter (hotspot vs non-hotspot)
Systematic artifact filter
Germline filters
1. If any normal exist -- (buffy coat and DMP normal) 2:1 rule
2. If not -- exac freq < 0.01% and VAF < 30%
CH tag

Usage

Default

Default options can be found

What `filter_calls.R` does

-- any call with occurrence in more than or equal to 2 donor samples (occurrence defined as more than or equal to 2 duplex reads)

We suggest that you filter out anything with duplex_support_num >= 2

-- reference for downstream analysis
Generate a
Read in and merging in

Example of the patient level table:

Filter Calls

Step 2 -- filtering

The second step takes all the genotypes generated from the first step and organized into a patient level variants table with VAFs and call status for each variant of each sample.

Each call is subjected to:

Read depth filter (hotspot vs non-hotspot)
Systematic artifact filter
Germline filters
1. If any normal exist -- (buffy coat and DMP normal) 2:1 rule
2. If not -- exac freq < 0.01% and VAF < 30%
CH tag

Usage

Default

Default options can be found

What `filter_calls.R` does

-- any call with occurrence in more than or equal to 2 donor samples (occurrence defined as more than or equal to 2 duplex reads)

We suggest that you filter out anything with duplex_support_num >= 2

-- reference for downstream analysis
Generate a
Read in and merging in

Example of the patient level table:

Call status annotation

All call passing read depth/genotype filter annotated as 'Called' or 'Genotyped'
Any call not satisfying germline filters are overwritten with 'Not Called'
1. Calls with zero coverage in plasma sample also annotated as 'Not Covered'

Rscript R/filter_calls.R -h                                         
usage: R/filter_calls.R [-h] [-m MASTERREF] [-o RESULTSDIR] [-dmpk DMPKEYPATH]
                        [-ch CHLIST] [-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
  -ch CHLIST, --chlist CHLIST
                        List of signed out CH calls [default]
  -c CRITERIA, --criteria CRITERIA
                        Calling criteria [default]

Rscript R/filter_calls.R -h                                         
usage: R/filter_calls.R [-h] [-m MASTERREF] [-o RESULTSDIR] [-dmpk DMPKEYPATH]
                        [-ch CHLIST] [-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
  -ch CHLIST, --chlist CHLIST
                        List of signed out CH calls [default]
  -c CRITERIA, --criteria CRITERIA
                        Calling criteria [default]

Filter Calls

hashtagUsage

hashtagDefault

hashtagWhat filter_calls.R does

hashtag

hashtagExample of the patient level table:

Filter Calls

hashtagUsage

hashtagDefault

hashtagWhat filter_calls.R does

hashtag

hashtagExample of the patient level table:

Usage

Default

What `filter_calls.R` does

Example of the patient level table:

Usage

Default

What `filter_calls.R` does

Example of the patient level table: