Pipeline Steps:

Call Somatic Structural Variants - DELLY workflow:

1. Calling Single Sample Somatic Structural Variants

delly call --genome hg38.fa --exclude hg38.excl --map-qual 20 --min-clique-size 5 --mad-cutoff 15 --outfile t1.bcf tumor1.bam normal1.bam

This step requires an aligned and sorted tumor sample BAM file and a matched normal sample as an input for variant calling with DELLY. The stringent filters (--map-qual 20 --min-clique-size 5 --mad-cutoff 15) are added, which can drastically reduce the runtime, especially when the input BAMs are big. In the pipeline, these filters are specified in the NextFlow input parameters config file. If need be, these stringent filters can be adjusted in the config file.

2. Query the generated bcfs to get the sample names, which will be used in step 3.

echo -e "tumor\ncontrol" > samples_type
bcftools query -l t1.bcf > samples_name
paste samples_name samples_type > samples.tsv

3. Somatic Filtering

delly filter -f somatic -o t1.pre.bcf -s samples.tsv t1.bcf

This step applies somatic filtering against the .bcf file generated in Step 1.

Note: cohort based false positive filtering is compuationally heavy and not implemented in this pipeline.

Call Somatic Structural Variants - Manta workflow:

1. Calling Single Sample Somatic Structural Variants

configManta.py --normalBam "${normal_bam}" --tumorBam "${tumor_bam}" --referenceFasta "${reference_fasta}" --runDir MantaWorkflow
MantaWorkflow/runWorkflow.py

This step requires an aligned and sorted tumor sample BAM file and a matched normal sample as an input for variant calling with Manta.