CallVariantsONT

CallVariants

descrition
A workflow for calling small and/or structural variants from an aligned ONT BAM file.

Inputs

Required

  • bai (File, required): ONT BAM index file
  • bam (File, required): ONT BAM file
  • call_small_variants (Boolean, required): Call small variants
  • call_small_vars_on_mitochondria (Boolean, required): if false, will not attempt to call variants on mitochondria
  • call_svs (Boolean, required): Call structural variants
  • fast_less_sensitive_sv (Boolean, required): to trade less sensitive SV calling for faster speed
  • prefix (String, required): Prefix for output files
  • ref_map_file (File, required): Table indicating reference sequence, auxillary file locations, and metadata.
  • run_dv_pepper_analysis (Boolean, required): to turn on DV-Pepper analysis or not (non-trivial increase in cost and runtime)
  • sample_id (String, required): Sample ID

Optional

  • dvp_memory (Int?): memory for DV-Pepper
  • dvp_threads (Int?): number of threads for DV-Pepper
  • ref_scatter_interval_list_ids (File?): A file that gives short IDs to the interval_list files; needed only when running DV-Pepper
  • ref_scatter_interval_list_locator (File?): A file holding paths to interval_list files; needed only when running DV-Pepper
  • sites_vcf (File?): for use with Clair
  • sites_vcf_tbi (File?): for use with Clair
  • tandem_repeat_bed (File?): BED file containing TRF finder for better PBSV calls (e.g. http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.trf.bed.gz)
  • Clair.chr (String?)
  • Clair.runtime_attr_override (RuntimeAttr?)
  • MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • MergeAndSortClairVCFs.header_definitions_file (File?)
  • MergeAndSortClairVCFs.runtime_attr_override (RuntimeAttr?)
  • MergeAndSortClair_gVCFs.header_definitions_file (File?)
  • MergeAndSortClair_gVCFs.runtime_attr_override (RuntimeAttr?)
  • MergeBams.runtime_attr_override (RuntimeAttr?)
  • MergeDeepVariantGVCFs.header_definitions_file (File?)
  • MergeDeepVariantGVCFs.runtime_attr_override (RuntimeAttr?)
  • MergeDeepVariantPhasedVCFs.header_definitions_file (File?)
  • MergeDeepVariantPhasedVCFs.runtime_attr_override (RuntimeAttr?)
  • MergeDeepVariantVCFs.header_definitions_file (File?)
  • MergeDeepVariantVCFs.runtime_attr_override (RuntimeAttr?)
  • MergePBSVVCFs.runtime_attr_override (RuntimeAttr?)
  • Pepper.runtime_attr_override (RuntimeAttr?)
  • SmallVariantsScatter.runtime_attr_override (RuntimeAttr?)
  • SmallVariantsScatterPrepp.runtime_attr_override (RuntimeAttr?)
  • Sniffles2SV.runtime_attr_override (RuntimeAttr?)
  • SubsetBam.runtime_attr_override (RuntimeAttr?)
  • ZipAndIndexPBSV.runtime_attr_override (RuntimeAttr?)
  • ZipAndIndexSnifflesVCF.runtime_attr_override (RuntimeAttr?)
  • size_balanced_scatter.runtime_attr_override (RuntimeAttr?)
  • PBSVslow.Call.runtime_attr_override (RuntimeAttr?)
  • PBSVslow.Discover.chr (String?)
  • PBSVslow.Discover.runtime_attr_override (RuntimeAttr?)
  • RunPBSV.Call.runtime_attr_override (RuntimeAttr?)
  • RunPBSV.Discover.chr (String?)
  • RunPBSV.Discover.runtime_attr_override (RuntimeAttr?)

Defaults

  • minsvlen (Int, default=50): Minimum SV length in bp (default: 50)
  • PickGcpZones.region (String, default="us-central1")
  • SmallVariantsScatter.prefix (String, default="subset"): Prefix for output files
  • SubsetBam.prefix (String, default="subset"): Prefix for output files

Outputs

  • sniffles_vcf (File?)
  • sniffles_tbi (File?)
  • pbsv_vcf (File?)
  • pbsv_tbi (File?)
  • clair_vcf (File?)
  • clair_tbi (File?)
  • clair_gvcf (File?)
  • clair_gtbi (File?)
  • dvp_phased_vcf (File?)
  • dvp_phased_tbi (File?)
  • dvp_g_vcf (File?)
  • dvp_g_tbi (File?)
  • dvp_vcf (File?)
  • dvp_tbi (File?)

Dot Diagram

CallVariantsONT