PfalciparumTypeDrugResistanceMarkers

PfalciparumTypeDrugResistanceMarkers

description
Workflow to generate a report of drug resistance markers

Inputs

Required

  • drug_resistance_list (File, required): List of drug resistance markers for which to search
  • gvcf (File, required): GVCF file to process to use for coverage analysis of drug resistance markers
  • gvcf_index (File, required): Index of the GVCF file to process
  • ref_map_file (File, required): Table indicating reference sequence, auxillary file locations, and metadata.
  • snpeff_db (File, required): SnpEff database for functional annotation
  • snpeff_db_identifier (String, required): Identifier for the SnpEff database to use
  • vcf (File, required): VCF file to process
  • vcf_index (File, required): Index of the VCF file to process

Optional

  • CallDrugResistanceMutations.runtime_attr_override (RuntimeAttr?)
  • CreateDrugResistanceSummary.runtime_attr_override (RuntimeAttr?)
  • FunctionallyAnnotateVariants.runtime_attr_override (RuntimeAttr?)

Defaults

  • do_functional_annotation (Boolean, default=true): Whether to perform functional annotation

Outputs

  • drug_resistance_summary (File)
  • drug_resistance_markers (File)
  • predicted_drug_status_chloroquine (String)
  • predicted_drug_status_pyrimethamine (String)
  • predicted_drug_status_sulfadoxine (String)
  • predicted_drug_status_mefloquine (String)
  • predicted_drug_status_artemisinin (String)
  • predicted_drug_status_piperaquine (String)
  • annotated_vcf (File)
  • annotated_vcf_index (File)
  • snpEff_summary (File?)
  • snpEff_genes (File?)
  • pfFd_Asp_193_Tyr (String)
  • pfaat1_Gln_454_Glu (String)
  • pfaat1_Lys_541_Asn (String)
  • pfaat1_Phe_313_Ser (String)
  • pfaat1_Ser_258_Leu (String)
  • pfap2_mu_Ile_592_Thr (String)
  • pfarps10_Val_127_Met (String)
  • pfatg18_Thr_38_Ile (String)
  • pfcarl_Ile_1139_Lys (String)
  • pfcarl_Leu_830_Val (String)
  • pfcarl_Ser_1076_Asn (String)
  • pfcarl_Ser_1076_Ile (String)
  • pfcarl_Val_1103_Leu (String)
  • pfcoronin_Arg_100_Lys (String)
  • pfcoronin_Glu_107_Val (String)
  • pfcoronin_Gly_50_Glu (String)
  • pfcoronin_Pro_76_Ser (String)
  • pfcrt_Asn_75_Glu (String)
  • pfcrt_Cys_101_Phe (String)
  • pfcrt_Cys_72_Ser (String)
  • pfcrt_Gly_353_Val (String)
  • pfcrt_His_97_Tyr (String)
  • pfcrt_Lys_76_Thr (String)
  • pfcrt_Met_343_Leu (String)
  • pfcrt_Met_74_Ile (String)
  • pfcrt_Phe_145_Ile (String)
  • pfcrt_Ser_350_Arg (String)
  • pfdhfr_Asn_51_Ile (String)
  • pfdhfr_Cys_50_Arg (String)
  • pfdhfr_Cys_59_Arg (String)
  • pfdhfr_Ile_164_Lys (String)
  • pfdhfr_Ser_108_Asn (String)
  • pfdhps_Ala_581_Gly (String)
  • pfdhps_Ala_613_Ser (String)
  • pfdhps_Ala_613_Thr (String)
  • pfdhps_Lys_437_Gly (String)
  • pfdhps_Lys_540_Glu (String)
  • pfdhps_Ser_436_Ala (String)
  • pfexo_Glu_415_Gly (String)
  • pfkelch13_Ala_675_Val (String)
  • pfkelch13_Arg_539_Thr (String)
  • pfkelch13_Arg_561_His (String)
  • pfkelch13_Arg_633_Ile (String)
  • pfkelch13_Asn_458_Tyr (String)
  • pfkelch13_Cys_580_Tyr (String)
  • pfkelch13_Ile_543_Thr (String)
  • pfkelch13_Met_476_Ile (String)
  • pfkelch13_Met_579_Ile (String)
  • pfkelch13_Phe_446_Ile (String)
  • pfkelch13_Phe_553_Leu (String)
  • pfkelch13_Phe_574_Leu (String)
  • pfkelch13_Phe_673_Ile (String)
  • pfkelch13_Pro_441_Ile (String)
  • pfkelch13_Pro_553_Leu (String)
  • pfkelch13_Pro_574_Leu (String)
  • pfkelch13_Tyr_493_His (String)
  • pfkelch13_Val_568_Gly (String)
  • pfmdr1_Asn_1024_Asp (String)
  • pfmdr1_Asn_86_Tyr (String)
  • pfmdr1_Asp_1246_Tyr (String)
  • pfmdr1_Ser_1034_Cys (String)
  • pfmdr1_Tyr_184_Phe (String)
  • pfmdr2_Thr_484_Ile (String)
  • pfubp1_Val_3275_Phe (String)

Dot Diagram

PfalciparumTypeDrugResistanceMarkers