Quality Control Metrics

ICGC ARGO provides access to data from ARGO member programs generated through the standardized ARGO Analysis pipelines. The following page lists quality control metrics analyses and data files generated by the ARGO Analysis pipelines.

Quality control metrics are collected and recorded at several checkpoints in the ARGO Analysis pipeline to ensure that only high-quality data is released. All QC Metrics are associated to a corresponding analysis/file set that they annotate.

Sequencing QC

Data files containing sequencing quality related metrics.

File Types

Data Subtypes	Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
Read Group Metrics	*.ubam_qc_metrics.tgz	Data files containing read group (lane) level QC metrics generated by Picard:CollectQualityYieldMetrics.	qc_metrics	Quality Control Metrics	DNA Seq Alignment

Aligned Reads QC

Data files containing various quality control metrics for aligned CRAM files.

File Types

Data Subtypes	Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
Alignment Metrics	*.qc_metrics.tgz	Data files containing comprehensive statistics for aligned CRAM files generated by Samtools:stats.	qc_metrics	Quality Control Metrics	DNA Seq Alignment
Alignment Metrics	*.bas_metrics.tgz	Data files containing comprehensive statistics for aligned CRAM files generated by Sanger:bam_stats.	qc_metrics	Quality Control Metrics	Sanger WGS Variant Calling Sanger WXS Variant Calling
Duplicates Metrics	*.duplicates_metrics.tgz	Data files containing duplicates metrics generated by biobambam2:bammarkduplicates2. Multiple reads that match at the same position in the genome are located and tagged as duplicate reads in the CRAM file, since duplicate reads are defined as originating from a single fragment of DNA.	qc_metrics	Quality Control Metrics	DNA Seq Alignment
OxoG Metrics	*.oxog_metrics.tgz	Data files containing OxoG metrics generated by GATK:CollectOxoGMetrics. OxoG quantifies the error rate resulting from oxidative artifacts for aligned CRAM files.	qc_metrics	Quality Control Metrics	DNA Seq Alignment

Analysis QC

Data files containing assessment metrics for various bioinformatics analysis quality control.

File Types

Data Subtypes	Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
Ploidy Tumour Purity	*.ascat_metrics.tgz	Data files containing tumour purity and ploidy estimated by Sanger ASCAT CNV caller.	qc_metrics	Quality Control Metrics	Sanger WGS Variant Calling
Genotyping Stats	*.genotyped_gender_metrics.tgz	Data files containing genotyping stats of CRAM files from the same donor generated by Sanger:compareBamGenotypes, including the fraction of matched genotypes and inferred donor gender.	qc_metrics	Quality Control Metrics	Sanger WGS Variant Calling
Variant Filtering Stats	*.mutect_filtering_metrics.tgz	Data file generated by GATK:FilterMutectCalls, including the information on the probability threshold chosen to optimize the F score and the number of false positives and false negatives for each filter to be expected from this choice.	qc_metrics	Quality Control Metrics	GATK Mutect2 Variant Calling
Variant Callable Stats	*.mutect_callable_metrics.tgz	Data file generated by GATK:Mutect2, containing number of sites that are considered callable for GATK Mutect2 calling with read depth equal to or higher than callable-depth of default 10.	qc_metrics	Quality Control Metrics	GATK Mutect2 Variant Calling
Runtime Stats	*.timings-supplement.tgz	Collected for different processing steps during the Sanger variant caller.	variant_calling_supplement	Quality Control Metrics	Sanger WGS Variant Calling Sanger WXS Variant Calling

Sample QC

Data files containing assessment metrics for sample quality control.

File Types

Data Subtypes	Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
Cross Sample Contamination	*.contamination_metrics.tgz	Data files containing cross sample contamination estimated by either Sanger:verifyBamHomChk or GATK:CalculateContamination , which provides information to determine whether the sample is possibly contaminated or swapped.	qc_metrics	Quality Control Metrics	Sanger WGS Variant Calling GATK Mutect2 Variant Calling