The first step of the pipeline is to genotype all the variants of interest in the included samples (this means plasma, buffy coat, DMP tumor, DMP normal, and donor samples). Once we obtained the read counts at every loci of every sample, we then generate a table of VAFs and call status for each variant in all samples within a patient in the next step.
Rscript R/compile_reads.R -h
usage: R/compile_reads.R [-h] [-m MASTERREF] [-o RESULTSDIR]
[-pb POOLEDBAMDIR] [-fa FASTAPATH]
[-gt GENOTYPERPATH] [-dmp DMPDIR] [-mb MIRRORBAMDIR]
[-dmpk DMPKEYPATH]
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
-pb POOLEDBAMDIR, --pooledbamdir POOLEDBAMDIR
Directory for all pooled bams [default]
-fa FASTAPATH, --fastapath FASTAPATH
Reference fasta path [default]
-gt GENOTYPERPATH, --genotyperpath GENOTYPERPATH
Genotyper executable path [default]
-dmp DMPDIR, --dmpdir DMPDIR
Directory of clinical DMP IMPACT repository [default]
-mb MIRRORBAMDIR, --mirrorbamdir MIRRORBAMDIR
Mirror BAM file directory [default]
-dmpk DMPKEYPATH, --dmpkeypath DMPKEYPATH
DMP mirror BAM key file [default]
Default options can be found here
compile_reads.R
doesgenotype-variants
| Sample_Barcode | duplex_bams | simplex_bams | standard_bam | Sample_Type | dmp_patient_id | | :--- | :--- | :--- | :--- | :--- | :--- | | plasma sample id | /duplex/bam | /simplex/bam | NA | duplex | P-xxxxxxx | | buffy coat id | NA | NA | /unfiltered/bam | unfilterednormal | P-xxxxxxx | | DMP Tumor ID | NA | NA | /DMP/bam | DMP_Tumor | P-xxxxxxx | | DMP Normal ID | NA | NA | /DMP/bam | DMP_Normal | P-xxxxxxx |
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