BroadOnPremMalariaPipeline_1_Alignment_and_Variant_Calling

BroadOnPremMalariaPipeline_1_Alignment

desciption
Recreation of the first and second steps of the Broad OnPrem Malaria Pipeline. Aligns reads and filters out human contamination, then calls variants and creates both a GVCF file and a recalibrated variants file.

Inputs

Required

  • contaminant_ref_map_file (File, required)
  • contaminant_ref_name (String, required)
  • ref_map_file (File, required)
  • resource_vcf_3d7_hb3 (File, required)
  • resource_vcf_3d7_hb3_index (File, required)
  • resource_vcf_7g8_gb4 (File, required)
  • resource_vcf_7g8_gb4_index (File, required)
  • resource_vcf_hb3_dd2 (File, required)
  • resource_vcf_hb3_dd2_index (File, required)
  • sample_name (String, required)

Optional

  • bai (File?)
  • bam (File?)
  • fq_end1 (File?)
  • fq_end2 (File?)
  • t_002_RevertSam.runtime_attr_override (RuntimeAttr?)
  • t_003_Bam2Fastq.bam_index (File?)
  • t_003_Bam2Fastq.reference_dict (File?)
  • t_003_Bam2Fastq.reference_fasta (File?)
  • t_003_Bam2Fastq.reference_fasta_index (File?)
  • t_003_Bam2Fastq.runtime_attr_override (RuntimeAttr?)
  • t_004_GetRawReadGroup.runtime_attr_override (RuntimeAttr?)
  • t_005_FilterOutHumanReads.runtime_attr_override (RuntimeAttr?)
  • t_006_AlignReads.runtime_attr_override (RuntimeAttr?)
  • t_008_SortAlignedBam.runtime_attr_override (RuntimeAttr?)
  • t_009_MarkDuplicates.read_name_regex (String?)
  • t_009_MarkDuplicates.runtime_attr_override (RuntimeAttr?)
  • t_009_MarkDuplicates.sorting_collection_size_ratio (Float?)
  • t_010_ReorderSam.runtime_attr_override (RuntimeAttr?)
  • t_011_RealignIndels.runtime_attr_override (RuntimeAttr?)
  • t_012_BQSR.runtime_attr_override (RuntimeAttr?)
  • t_012_IndexRealignIndels.runtime_attr_override (RuntimeAttr?)
  • t_013_HaplotypeCaller.runtime_attr_override (RuntimeAttr?)
  • t_013_IndexBQSR.runtime_attr_override (RuntimeAttr?)
  • t_014_HaplotypeCallerGvcfMode.runtime_attr_override (RuntimeAttr?)
  • t_015_VariantRecalibrator.runtime_attr_override (RuntimeAttr?)
  • t_016_SortCompressIndexRawVCF.runtime_attr_override (RuntimeAttr?)
  • t_017_SortCompressIndexVCF.runtime_attr_override (RuntimeAttr?)
  • t_018_SortCompressIndexGVCF.runtime_attr_override (RuntimeAttr?)

Defaults

  • t_001_WdlExecutionStartTimestamp.date_format (String, default="%Y%m%d_%H%M%S_%N")
  • t_013_HaplotypeCaller.gvcf_mode (Boolean, default=false)

Outputs

  • raw_vcf (File)
  • raw_vcf_index (File)
  • recalibrated_vcf (File)
  • recalibrated_vcf_index (File)
  • gvcf (File)
  • gvcf_index (File)

Dot Diagram

BroadOnPremMalariaPipeline_1_Alignment_and_Variant_Calling