Add strelka2 to pipeline

[iskandr]

I'm currently running Strelka2 in these two steps:

1) Create a Python file to run Strelka2:

configureStrelkaSomaticWorkflow.py \
            --normalBam $NORMAL_BAM \
            --tumorBam $TUMOR_BAM \
            --referenceFasta $REFERENCE_FASTA_PATH \
            --exome \
        --runDir $STRELKA_DIR";

2) Run the generated Python file

python runWorkflow.py \
                -m local \
                -j $NUMBER_PROCESSORS \
                -g $MEMORY_LIMIT_AS_INTEGER

[iskandr]

There's also an equivalent configureStrelkaGermlineWorkflow.py

[iskandr]

The --exome flag gets rid of any filtering assumptions about how the depth of a site should relate to the average depth on a chromosome. If you drop the flag then it assumes you have WGS data with relatively uniform coverage.

[iskandr]

The germline pipeline can take multiple BAMs and then the generated gVCF will have a sample column for each BAM. The gVCF is gigantic btw.