ONTPepper

Pepper

description

A 1-stop shop task offered by Pepper for ONT data. This pipeline calls small variants using DeepVariant.

Inputs

Required

• bai (File, required): The input bam index file.
• bam (File, required): The input bam file.
• memory (Int, required): The amount of memory to use.
• ref_fasta (File, required): The reference fasta file.
• ref_fasta_fai (File, required): The reference fasta index file.
• threads (Int, required): The number of threads to use.

Optional

• runtime_attr_override (RuntimeAttr?): override the default runtime attributes

Defaults

• zone_string (String, default="us-central1-c us-central1-f us-central1-a us-central1-b"): select which zone (GCP) to run this task

Outputs

• VCF (File)
• VCF_tbi (File)
• gVCF (File)
• gVCF_tbi (File)
• phasedVCF (File)
• phasedtbi (File)
• hap_tagged_bam (File)
• hap_tagged_bai (File)
• output_dir_structure (File)
• phaseset_bed (File)
• visual_report_html (File)