BroadOnPremMalariaPipeline_2_JointVariantCalling

BroadOnPremMalariaPipeline_2_JointVariantCalling

desciption

Recreation of the second step of the Broad OnPrem Malaria Pipeline. Joint calls and recalibrates/filters variants.

Inputs

Required

• ref_map_file (File, required)
• resource_vcf_3d7_hb3 (File, required)
• resource_vcf_7g8_gb4 (File, required)
• resource_vcf_hb3_dd2 (File, required)
• sample_name (String, required)
• vcf_files (Array[File], required)
• vcf_index_files (Array[File], required)
• t_002_VariantRecalibrator.resource_vcf_3d7_hb3_index (File, required)
• t_002_VariantRecalibrator.resource_vcf_7g8_gb4_index (File, required)
• t_002_VariantRecalibrator.resource_vcf_hb3_dd2_index (File, required)

Optional

• t_001_GenotypeGVCFs.runtime_attr_override (RuntimeAttr?)
• t_002_VariantRecalibrator.runtime_attr_override (RuntimeAttr?)
• t_003_SortCompressIndexVcf.runtime_attr_override (RuntimeAttr?)

Outputs

• joint_vcf (File)
• joint_vcf_index (File)

Dot Diagram