CEN GRCh38 v1.0.0

Release file: WES_multiqc_config_GRCh38_v1.0.0.yaml

Changes (compared to GRCh37)

• Updates FREEMIX threshold
• Updates PCT_TARGET_BASES_20X threshold (and updates format to 2dp)
• Updates FOLD_ENRICHMENT threshold (and updates format to 2dp)
• Updates eggd_vcf_qc field names to match v2.0.0+
• Updates eggd_vcf_qc mean_het threshold (and updates format to 4dp and specifies column ordering to match what is currently shown in MultiQC report in GRCh37)
• New Sentieon insert size warning threshold
• Updates hap.py thresholds
• Update Somalier section name from 'Somalier Sex Check' -> 'Somalier'

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3558539817/CEN_multiqc_config_GRCh38_v1.0.0.yaml

TWE_config_GRCh38_v1.0.0

Release file: WES_multiqc_config_GRCh38_v1.0.0.yaml

Changes (compared to GRCh37)

• Updates FREEMIX threshold
• Updates PCT_TARGET_BASES_20X threshold (and updates format to 2dp)
• Updates FOLD_ENRICHMENT threshold (and updates format to 2dp)
• Updates eggd_vcf_qc field names to match v2.0.0+
• Updates eggd_vcf_qc mean_het threshold (and updates format to 4dp and specifies column ordering to match what is currently shown in MultiQC report in GRCh37)
• New Sentieon insert size warning threshold
• Updates hap.py thresholds
• Update Somalier section name from 'Somalier Sex Check' -> 'Somalier'

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3517087772/WES_multiqc_config_GRCh38_v1.0.0.yaml

TSO500_v2.1.0

Changes

• Rename TSO500_multiqc_config_v2.0.0.yaml to TSO500_multiqc_config_v2.1.0.yaml
• Included a custom_data section containing the metrics from the MetricsOutput.tsv file for both DNA and RNA
• Included table_cond_formatting_rules section containing the warning thresholds for the different metrics
• Specified the metricsoutput_dna (MetricsOutput_MultiQC_DNA.tsv) and metricsoutput_rna (MetricsOutput_MultiQC_RNA.tsv) inputs in the sp and dx_sp sections for MultiQC to call

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3369041924/TSO500_multiqc_config_v2.1.0.yaml
Note: testing was done on merged config from eggd_001_Reference, but this config is identical. See Jira ticket for evidence.

TWE_config_v2.3.0

Changes

• Remove older versions of WES config (v1.0.0, v1.0.1, v1.0.2 and v2.1.0) from repo
• Rename WES_multiqc_config_v2.2.0.yaml to WES_multiqc_config_v2.3.0.yaml
• Add eggd_sex_check output, *_mqc.json to dx search pattern

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3308814370/WES_multiqc_config_v2.3.0.yaml

CEN_config_v2.3.0

Changes

• Remove older versions of CEN config (v1.0.0, v2.0.0, and v2.1.0) from repo
• Rename CEN_multiqc_config_v2.2.0.yaml to CEN_multiqc_config_v2.3.0.yaml
• Add eggd_sex_check output, *_mqc.json to dx search pattern

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3317432330/CEN_multiqc_config_v2.3.0.yaml

TWE v2.1.0

Release file: WES_multiqc_config_v2.1.0.yaml

Changes:

• updated dx_sp section to conform with the output directory structure generated by eggd_conductor during automated processing.
• force plots to be interactive
• add a Y-scale to Sentieon/Picard GC bias plots
• update the description text for the verifybamid module
• removed whitespace

Development and testing documented: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/2921332737/TWE+MultiQC+config+file+v2.1.0

CEN v2.1.0

Release file: CEN_multiqc_config_v2.1.0.yaml

Changes:

• updated dx_sp section to conform with the output directory structure generated by eggd_conductor during automated processing.
• force plots to be interactive
• add a Y-scale to Sentieon/Picard GC bias plots
• update the description text for the verifybamid module
• removed whitespace

Development and testing documented:

https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/2919137281/CEN+MultiQC+config+file+v2.1.0