PLASTER is a comprehensive data processing pipeline for allele typing from long amplicon sequencing data generated on the PacBio SMRT platform. Inputs are PacBio subreads in BAM format, as well as sample barcodes and target amplicon details. Outputs are phased BAMs for each sample amplicon and variant calls in VCF format. Additionally the pipeline supports Pharmacogenomic star alelle assignment using the PharmVar database, and gene fusion detection for CYP2D6 and CYP2D7 fusion alleles.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a portable and efficient manner. Included is a Docker container, making installation trivial and results highly reproducible.
Running the test dataset
nextflow run bahlolab/PLASTER -profile preproc,test,singularity
This command will download the pipeline from GitHub and run the pre-processing stage on a minimal test dataset using singularity to run the software container. Replace "singularity" with "docker" to use docker instead. Note that nextflow pipelines are run in the current working directory, so make sure your terminal is in the appropriate directory first.
Profiles are provided for executors SLURM and PBS/torque, to use these append either slurm
or pbs
to the end of the profile specification (e.g., -profile preproc,test,singularity,slurm
). Additional executors may be specified in a custom nextflow configuration, see Nextflow executor documentation.
nextflow run bahlolab/PLASTER -profile preproc,singularity -c <my_dataset.config>
where my_dataset.config
is a Nextflow config file specifying the following required parameters:
params {
subreads_bam = '/PATH/TO/MY/subreads.bam'
barcodes_fasta = '/PATH/TO/MY/barcodes.fasta'
amplicons_json = '/PATH/TO/MY/amplicons.json'
ref_fasta = 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr22.fa.gz'
}
See Pre-processing Parameters for more details, including details on running in single-sample mode (no barcodes).
-resume
option to the Nextflow run command will use cached results from any pipeline steps where the inputs remain the same:
nextflow run bahlolab/PLASTER -profile preproc,singularity -c <my_dataset.config> -resume
./output/bam/
./output/sample_amplicon_bam_manifest.csv
./output/pre_processing_report.html
Running the test dataset
nextflow run bahlolab/PLASTER -profile typing,test,singularity
This command will download the pipeline from GitHub and run the allele-typing stage on a minimal test dataset using singularity to run the software container. Replace "singularity" with "docker" to use docker instead. Note that nextflow pipelines are run in the current working directory, so make sure your terminal is in the appropriate directory first.
Profiles are provided for executors SLURM and PBS/torque, to use these append either slurm
or pbs
to the end of the profile specification (e.g., -profile preproc,test,singularity,slurm
). Additional executors may be specified in a custom nextflow configuration, see Nextflow executor documentation.
nextflow run bahlolab/PLASTER -profile typing,singularity -c <my_dataset.config>
where my_dataset.config
is a file specifying the following required parameters:
params {
manifest = '/PATH/TO/MY/manifest.csv'
amplicons_json = '/PATH/TO/MY/amplicons.json'
ref_fasta = 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr22.fa.gz'
}
See Allele-typing Parameters for more details.
-resume
option to the Nextflow run command will use cached results from any pipeline steps where the inputs remain the same:
nextflow run bahlolab/PLASTER -profile preproc,singularity -c <my_dataset.config> -resume
./output/low_read_count.csv
./output/low_phased_read_count.csv
./output/fusion_calls.csv
./output/fusion_report.html
./output/<amplicon>.phase_copy_num.csv
./output/AmpPhaseR/
./output/<amplicon>.vep.vcf.gz
./output/<amplicon>.sample_phase_alleleles.csv
./output/<amplicon>.allele_definition.csv
pb_ccs.nf
pb_lima.nf
pb_mm2.nf
bam_annotate_amplicons.py
based on pysambam_annotate_samples.py
and bam_split_sample_amplicons.py
based on pysampreproc-report.Rmd
fusion_call.R
and Rmarkdown document fusion_report.Rmd
gatk.nf
phase.nf
gatk.nf
vep.nf
pharmvar_star_allele.R
using PharmVar databaseCopyNumAnalysis
contains raw data and the analysis Rmarkdown document associated with the qPCR copy number analysis presented in the PLASTER manuscript.