Shallow WGS Pipeline

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, mutect2).

Note: to process BAMs produced elsewhere, you MUST have the identical reference used for alignment OR be prepared to subset each BAM to contigs present in your desired reference file (ie, you can not process BAMs aligned by TGL using the hg38 reference on H4H [igenome-human/hg38]!!)

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

Pre-processing steps

run fastq to remove adapter sequences from fastq files

perl trim_adapters.pl \
-t /path/to/swgs_pipeline_config.yaml \
-d /path/to/fastq_dna_config.yaml \
-o /path/to/output/fastq_trimmed \
-b /path/to/output/fastq_trimmed/trimmed_fastq_files.yaml \
-c slurm \
--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 fastqc to summarize trimmed fastq QC metrics

perl fastqc.pl \
-t /path/to/swgs_pipeline_config.yaml \
-d /path/to/output/fastq_trimmed/trimmed_fastq_files.yaml \
-o /path/to/output/fastqc \
-c slurm \
--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 BWA to align to a reference genome

perl bwa.pl \
-t /path/to/swgs_pipeline_config.yaml \
-d /path/to/output/fastq_trimmed/trimmed_fastq_files.yaml \
-o /path/to/output/BWA \
-b /path/to/output/BWA/bwa_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 }

QC steps

once BWA has finished, get BAM QC metrics

perl get_sequencing_metrics.pl \
-t /path/to/swgs_pipeline_config.yaml \
-d /path/to/output/BWA/bwa_bam.yaml \
-o /path/to/output/BAMQC \
-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 }

Variant calling steps

Tumour Fraction estimates

run ichorCNA to estimate tumour fractions

perl ichor_cna.pl \
-t /path/to/swgs_pipeline_config.yaml \
-d /path/to/output/BWA/bwa_bam.yaml \
-o /path/to/output/IchorCNA \
-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 }