multiqc_config.yml

title: "LUMC PGx"
subtitle: "MultiQC report for the PacBio-variantcalling pipeline"
intro_text: "This report contains QC data for the tools that are part of the PacBio-variantcalling pipeline. Reads are mapped against the reference using pbmm2, and variants are called using GATK4 or DeepVariant. Finally, phased BAM and VCF files are generated using WhatsHap."
report_comment: "The sections under the PGx heading are custom for this project, all other reports are part MultiQC itself"

report_header_info:
  - Pipeline: 'https://github.com/LUMC/PacBio-variantcalling'
  - Platform: 'PacBio HiFi'
  - Project: 'LUMC PGx'

show_analysis_paths: False

table_columns_visible:
  HSMetrics:
    BAIT_DESIGN_EFFICIENCY: False
    MEAN_BAIT_COVERAGE: False
    NEAR_BAIT_BASES: False
    OFF_BAIT_BASES: False
    PCT_USABLE_BASES_ON_BAIT: False
    ON_BAIT_BASES: False
    ON_BAIT_VS_SELECTED: False
  Picard:
    PCT_PF_READS_ALIGNED: False
    FOLD_ENRICHMENT: False
  WhatsHap:
    variants: True


table_columns_placement:
  HsMetrics:
    PCT_USABLE_BASES_ON_TARGET: 900
    ZERO_CVG_TARGETS_PCT: 901
    FOLD_ENRICHMENT: 902
    MEAN_TARGET_COVERAGE: 903
    MEDIAN_TARGET_COVERAGE: 904
    PF_READS: 905
    PF_UNIQUE_READS: 906
    ON_TARGET_BASES: 907