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Prerequisites

SMuRF depends on the output from the bcbio-nextgen variant2 workflow with the following options set in the bcbio-nextgen configuration YAML file:

• mark_duplicates: true
• recalibrate: false
• realign: gatk
• remove_lcr: false
• variantcaller: [mutect2,freebayes,vardict,varscan,strelka2]

Furthermore, to ensure compatibility, make sure you are using the SMuRF software version that has been tested with a given bcbio-nextgen software version.

SMuRF	Trained and verified on bcbio-nextgen
v1.0	v1.0.0
v1.4	v1.0.3
v1.6	v1.0.8
v2.0	v1.1.5
v3.0	v1.2.9