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)

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)