SRUtils

BamToFq

Inputs

Required

  • bam (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="out")

Outputs

  • fq_end1 (File)
  • fq_end2 (File)
  • fq_unpaired (File)

FixMate

Inputs

Required

  • input_bam (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="out")

Outputs

  • bam (File)

Bam2FqPicard

Inputs

Required

  • bam (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="out")

Outputs

  • fastq (File)

BwaMem2

Inputs

Required

  • fq_end1 (File, required)
  • fq_end2 (File, required)
  • ref_0123 (File, required)
  • ref_amb (File, required)
  • ref_ann (File, required)
  • ref_bwt (File, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_index (File, required)
  • ref_pac (File, required)

Optional

  • read_group (String?)
  • runtime_attr_override (RuntimeAttr?)

Defaults

  • mark_short_splits_as_secondary (Boolean, default=false)
  • prefix (String, default="out")

Outputs

  • bam (File)

Bowtie2

Inputs

Required

  • fq_end1 (File, required): FASTQ file containing end 1 of reads.
  • fq_end2 (File, required): FASTQ file containing end 2 of reads.
  • prefix (String, required): Prefix for output files.
  • ref_bowtie_indices (Array[File], required): Bowtie2 indices for the given genome.
  • ref_fasta (File, required): Reference FASTA file for the genome of the organism to which to align reads.
  • ref_fasta_index (File, required): Reference FASTA index file for the genome of the organism to which to align reads.

Optional

  • rg_id (String?)
  • rg_lb (String?)
  • rg_pl (String?)
  • rg_sm (String?)
  • runtime_attr_override (RuntimeAttr?): Optional override for runtime attributes.

Defaults

  • skip_sort (Boolean, default=false)

Outputs

  • bam (File)
  • bai (File)

MergeBamAlignment

Inputs

Required

  • aligned_bam (File, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_index (File, required)
  • unaligned_bam (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="out")

Outputs

  • bam (File)

MarkDuplicates

Inputs

Required

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

Optional

  • read_name_regex (String?)
  • runtime_attr_override (RuntimeAttr?)
  • sorting_collection_size_ratio (Float?)

Outputs

  • bam (File)
  • metrics (File)

BaseRecalibrator

Inputs

Required

  • input_bam (File, required); localization_optional: true
  • input_bam_index (File, required)
  • known_sites_index (File, required)
  • known_sites_vcf (File, required)
  • prefix (String, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_index (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Outputs

  • recalibration_report (File)

ApplyBQSR

Inputs

Required

  • input_bam (File, required); localization_optional: true
  • input_bam_index (File, required)
  • prefix (String, required)
  • recalibration_report (File, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_index (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • bin_base_qualities (Boolean, default=true)
  • emit_original_quals (Boolean, default=true)

Outputs

  • recalibrated_bam (File)
  • recalibrated_bai (File)

RevertSam

Inputs

Required

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

Optional

  • runtime_attr_override (RuntimeAttr?)

Outputs

  • bam (File)

ComputeBamStats

Inputs

Required

  • bam_file (File, required)

Optional

  • qual_threshold (Int?)
  • runtime_attr_override (RuntimeAttr?)

Outputs

  • results (Map[String,Float])
  • results_file (File)

MergeVCFs

description
Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs

Inputs

Required

  • input_vcfs (Array[File], required)
  • input_vcfs_indexes (Array[File], required)
  • prefix (String, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • is_gvcf (Boolean, default=false)

Outputs

  • output_vcf (File)
  • output_vcf_index (File)

IndexFeatureFile

description
Create a Tribble index for a feature file using GATK. Feature files are defined inside GATK and include VCF, BED, GTF, and other files.

Inputs

Required

  • feature_file (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Outputs

  • index (File)

RevertBaseQualities

description
Replace base qualities in the bam file with those located in the OQ tag. If ApplyBQSR has not been run on the given bam file, no changes are made and the original file is returned.

Inputs

Required

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

Optional

  • bai (File?)
  • runtime_attr_override (RuntimeAttr?)

Outputs

  • bam_out (File)
  • bai_out (File)