Running individual tools (RNA)

Running individual steps

Sometimes, you may only want to run one or a few steps, rather than the full pipeline (ie, alignment), or you may already have BAMs (aligned elsewhere) and want to run a specific variant calling tool (ie, rsem).

In all cases, tools will write individual commands to file: /path/to/output/directory/TOOL/logs/run_tool_step_sample/script.sh

run STAR to align to a reference genome

perl star.pl \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/fastq_rna_config.yaml \
-o /path/to/output/directory/STAR \
-b /path/to/output/bam.yaml \
-c slurm \
--remove \
--dry-run { if this is a dry-run } \
--no-wait { if not a dry-run and you don't want to wait around for it to finish }

run Arriba on raw FASTQ data

perl arriba.pl \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/fastq_rna_config.yaml \
-o /path/to/output/directory/Arriba \
-c slurm \
--remove \
--dry-run { if this is a dry-run } \
--no-wait { if not a dry-run and you don't want to wait around for it to finish }

run Fusioncatcher on raw FASTQ data

perl fusioncatcher.pl \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/fastq_rna_config.yaml \
-o /path/to/output/directory/FusionCatcher \
-c slurm \
--remove \
--dry-run { if this is a dry-run } \
--no-wait { if not a dry-run and you don't want to wait around for it to finish }

run RSEM on STAR-aligned BAMs

perl rsem.pl \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/star_bam_config.yaml \
-o /path/to/output/directory/RSEM \
-c slurm \
--remove \
--dry-run { if this is a dry-run } \
--no-wait { if not a dry-run and you don't want to wait around for it to finish }

run STAR-Fusion on STAR-aligned BAMs

perl star_fusion.pl \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/star_bam_config.yaml \
-o /path/to/output/directory/STAR-Fusion \
-c slurm \
--remove \
--dry-run { if this is a dry-run } \
--no-wait { if not a dry-run and you don't want to wait around for it to finish }

run GATK split CIGAR, indel realignment and base quality score recalibration on MarkDup BAMs

perl gatk.pl \
--rna \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/star/bam_config.yaml \
-o /path/to/output/directory/GATK \
-b /path/to/output/bam.yaml \
-c slurm \
--remove \
--dry-run { if this is a dry-run } \
--no-wait { if not a dry-run and you don't want to wait around for it to finish }

run GATK HaplotypeCaller, variant filtration and annotataion

perl haplotype_caller.pl \
--rna \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/gatk_bam_config.yaml \
-o /path/to/output/directory/HaplotypeCaller \
-c slurm \
--remove \
--dry-run { if this is a dry-run } \
--no-wait { if not a dry-run and you don't want to wait around for it to finish }

summarize output and create final report

perl pughlab_pipeline_auto_report.pl \
--create_report \
-t /path/to/rna_pipeline_config.yaml \
-d /path/to/bam_config.yaml \
-c slurm \
--dry-run

This report generator is still a work in progress and may not run correctly if only a subset of tools were run!