Flare

PrepStudyVcfForFlare

Inputs

Required

• joint_vcf (File, required)
• prefix (String, required)
• ref_fasta (File, required)
• ref_fasta_fai (File, required)

Defaults

• maf (Float, default=0.01)

Outputs

• gt_bcf (File)
• gt_bcf_csi (File)

PrepRefVcfForFlare

Inputs

Required

• prefix (String, required)
• ref_vcf (File, required)

Outputs

• ref_bcf (File)
• ref_bcf_csi (File)

IntersectVCFsForFlare

Inputs

Required

• gt_vcf (File, required)
• gt_vcf_index (File, required)
• prefix (String, required)
• ref_vcf (File, required)
• ref_vcf_index (File, required)

Outputs

• gt_vcf_out (File)
• gt_vcf_csi (File)
• ref_vcf_out (File)
• ref_vcf_csi (File)

ThinVCFsForFlare

Inputs

Required

• gt_vcf (File, required)
• prefix (String, required)
• ref_vcf (File, required)

Defaults

• thin_bp (Int, default=20000)

Outputs

• gt_vcf_out (File)
• gt_vcf_csi (File)
• ref_vcf_out (File)
• ref_vcf_csi (File)

FilterFlareReadySites

Inputs

Required

• gt_vcf (File, required)
• gt_vcf_index (File, required)
• prefix (String, required)
• ref_panel (File, required)
• ref_vcf (File, required)
• ref_vcf_index (File, required)

Outputs

• gt_vcf_out (File)
• gt_vcf_csi (File)
• ref_vcf_out (File)
• ref_vcf_csi (File)

MergeGlobalAncestry

Inputs

Required

• global_anc_files (Array[File], required)
• prefix (String, required)

Outputs

• global_ancestry_tsv (File)

Flare

description

Local Ancestry Inference

Inputs

Required

• output_prefix (String, required)
• plink_map (File, required)
• ref_panel (File, required)
• ref_vcf (File, required)
• ref_vcf_index (File, required)
• test_vcf (File, required)
• test_vcf_index (File, required)

Optional

• flare_model (File?)
• runtime_attr_override (RuntimeAttr?)

Defaults

• em (Boolean, default=true)
• mem_gb (Int, default=64)
• nthreads (Int, default=16)
• zones (String, default="us-central1-a us-central1-b us-central1-c us-central1-f")

Outputs

• global_anc (File)
• model (File)
• anc_vcf (File)
• log (File)