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

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

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

For each patient

• Create a sample sheet -- similar to the one for genotype-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

• Generate all variants of interests

  • DMP calls from cbio repo

  • ACCESS calls from SNV pipeline

• Generate unique variants list

• Tag hotspots on unique variants

• Genotype with genotype-variants

Afterwards, for donor bams

• Obtain all variants genotyped in any patient, generate a all unique list of variants

• Genotype with genotype-variants