WGS_preprocessing#

Inputs#

Required#

  • dbSNP_vcf (File, required)

  • dbSNP_vcf_index (File, required)

  • input_cram (File, required)

  • input_cram_index (File, required)

  • known_indels_sites_VCFs (Array[File], required)

  • known_indels_sites_indices (Array[File], required)

  • preemptible_tries (Int, 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_name (String, required)

  • ref_pac (File, required)

  • ref_sa (File, required)

  • sample_name (String, required)

Optional#

  • ref_alt (File?)

  • CramToBam.reference_index (File?)

  • CramToBam.runtime_attr_override (RuntimeAttr?)

Defaults#

  • requester_pays (Boolean, default=false)

  • samtools_docker (String, default=”biocontainers/samtools:v1.9-4-deb_cv1”)

  • unmapped_bam_suffix (String, default=”.bam”)

  • BamToUnmappedBams.additional_disk_size (Int, default=20)

  • BamToUnmappedBams.gatk_docker (String, default=”broadinstitute/gatk:latest”)

  • BamToUnmappedBams.gatk_path (String, default=”/gatk/gatk”)

  • PreProcessingForVariantDiscovery_GATK4.agg_large_disk (Int, default=400)

  • PreProcessingForVariantDiscovery_GATK4.agg_medium_disk (Int, default=300)

  • PreProcessingForVariantDiscovery_GATK4.agg_small_disk (Int, default=200)

  • PreProcessingForVariantDiscovery_GATK4.bwa_commandline (String, default=”bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta”)

  • PreProcessingForVariantDiscovery_GATK4.compression_level (Int, default=5)

  • PreProcessingForVariantDiscovery_GATK4.flowcell_medium_disk (Int, default=200)

  • PreProcessingForVariantDiscovery_GATK4.flowcell_small_disk (Int, default=100)

  • PreProcessingForVariantDiscovery_GATK4.gatk_docker (String, default=”us.gcr.io/broad-gatk/gatk:4.2.0.0”)

  • PreProcessingForVariantDiscovery_GATK4.gatk_path (String, default=”/gatk/gatk”)

  • PreProcessingForVariantDiscovery_GATK4.gotc_docker (String, default=”us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.7-1603303710”)

  • PreProcessingForVariantDiscovery_GATK4.gotc_path (String, default=”/usr/gitc/”)

  • PreProcessingForVariantDiscovery_GATK4.python_docker (String, default=”python:2.7”)

  • BamToUnmappedBams.RevertSam.machine_mem_gb (Int, default=2)

  • BamToUnmappedBams.RevertSam.preemptible_attempts (Int, default=3)

  • BamToUnmappedBams.SortSam.machine_mem_gb (Int, default=4)

  • BamToUnmappedBams.SortSam.preemptible_attempts (Int, default=3)

  • PreProcessingForVariantDiscovery_GATK4.ApplyBQSR.mem_size_gb (Float, default=4)

  • PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator.mem_size_gb (Float, default=6)

  • PreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV.mem_size_gb (Float, default=2)

  • PreProcessingForVariantDiscovery_GATK4.GatherBamFiles.mem_size_gb (Float, default=3)

  • PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports.mem_size_gb (Float, default=4)

  • PreProcessingForVariantDiscovery_GATK4.GetBwaVersion.mem_size_gb (Float, default=1)

  • PreProcessingForVariantDiscovery_GATK4.MarkDuplicates.mem_size_gb (Float, default=7.5)

  • PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment.mem_size_gb (Float, default=4)

  • PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.mem_size_gb (Float, default=14)

  • PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.num_cpu (String, default=16)

  • PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.mem_size_gb (Float, default=10)

Outputs#

  • duplication_metrics (File)

  • bqsr_report (File)

  • analysis_ready_bam (File)

  • analysis_ready_bam_index (File)

  • analysis_ready_bam_md5 (File)