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:
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]
Default options can be found here
filter_calls.R
doesGenerate a reference of systematic artifacts -- any call with occurrence in more than or equal to 2 donor samples (occurrence defined as more than or equal to 2 duplex reads)
{% hint style="info" %} We suggest that you filter out anything with duplex_support_num >= 2 {% endhint %}
| Hugo_Symbol | Start_position | Variant_Classification | Other variant descriptions | ... | C-xxxxxx-L001-d___duplex.called | C-xxxxxx-L001-d___duplex.total | C-xxxxxx-L002-d___duplex.called | C-xxxxxx-L001-d___duplex.total | C-xxxxxx-N001-d___unfilterednormal | P-xxxxxxx-T01-IM6___DMP_Tumor | P-xxxxxxx-T01-IM6___DMP_Normal | | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | | KRAS | xxxxxx | Missense Mutation | ... | ... | Called | 15/1500(0.01) | Not Called | 0/1800(0) | 0/200(0) | 200/800(0.25) | 1/700(0.001) |
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