Compile Reads Step 1 -- intra-patient genotyping
There are two variantion:
compile_reads.R : Works with Research ACCESS and Clinical IMPACT
compile_reads_all.R: Works with Research ACCESS, Clinical ACCESS and Clinical IMPACT
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.
Usage compile_reads.R
Copy 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] Usage compile_reads_all.R
Copy Rscript R/compile_reads_all.R -h
usage: R/compile_reads_all.R [-h] [-m MASTERREF] [-o RESULTSDIR]
[-pid PROJECTID] [-pb POOLEDBAMDIR]
[-fa FASTAPATH] [-gt GENOTYPERPATH] [-dmp DMPDIR]
[-mb MIRRORBAMDIR] [-mab MIRRORACCESSBAMDIR]
[-dmpk DMPKEYPATH] [-dmpak DMPACCESSKEYPATH]
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
-pid PROJECTID, --projectid PROJECTID
Project ID for submitted jobs involved in this run
-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 repository [default]
-mb MIRRORBAMDIR, --mirrorbamdir MIRRORBAMDIR
Mirror BAM file directory [default]
-mab MIRRORACCESSBAMDIR, --mirroraccessbamdir MIRRORACCESSBAMDIR
Mirror BAM file directory for MSK-ACCESS [default]
-dmpk DMPKEYPATH, --dmpkeypath DMPKEYPATH
DMP mirror BAM key file [default]
-dmpak DMPACCESSKEYPATH, --dmpaccesskeypath DMPACCESSKEYPATH
DMP mirror BAM key file for MSK-ACCESS [default] Default
Default options can be found here
What compile_reads does