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Nucleo Quality Control

Workflows that generates, aggregates, and visualizes quality control files for CMO-CH.

Introduction

This section aims to provide an introduction to the Nucleo Quality Control process along with installation and running instructions. The Nucleo QC process generated QC metrics for all type of BAM files generated by Nucleo, including collapsed, uncollapsed, duplex and simplex BAM files. The main outputs of the workflow are the MultiQC report and coverage report. Thorough intepretation of the output files can be found in this gitbook section.

Credits

CMO cfDNA Informatics Team
Clinical Bioinformatics

Workflow description

Nucleo QC tools, subworkflows and main workflows organization

The workflows for nucleo quality control are written in the common workflow language (CWL). Below, figure 1 illustrates the organization level, all tools used in the bigger workflows are listed first, this tools are then called in the subworkflows listed second, then the subworfklows are called to make bigger main workflows.

For instance, in the qc_collapsed subworkflows we are using multiple command line tools such as all the biometrics tools. The main workflow to generate all the QC outputs is nucleo_qc seen at the bottom in the high-level CWL workflow section. This workflow calls both the nucleo_qc_generator.cwl that generates the QC results for each BAM file (collapsed, uncollapsed, duplex and simplex) by calling all the subworkflows and nucleo_aggregate_visualize.cwl that aggregates the QC results into different folders and calls MultiQC to generate the html QC report.

For individuals/groups that do not require a multiqc report and would like to generate their own QC reports, you may use generate_aggregate.cwl instead of nucleo_qc.cql as this will generate all QC results apart from the MultiQC html report.

Requirements

Before installing the pipeline, make sure your system supports these requirements

The following are the requirements for running the workflow:

A system with either or

Installation and Usage

You must have run the main Nucleo workflow first before running the Nucleo QC workflows.

Step 1: Create a virtual environment.

Option (A) - if using cwltool

Workflow inputs

Description of Nucleo QC workflow inputs

Parameter Used by Tools

Common Parameters Across Tools

Input for nucleo_qc.cwl

Option 1: Input.yml example to run workflow enable mosdepth/athena to create coverage reports

Input for nucleo_aggregate_visualize.cwl

Workflow outputs

The workflow outputs multiple QC metric files that are merged into a single MultiQC report. The workflow also outputs the athena coverage report. For further interpretation please use the link to and .

Nucleo_qc.cwl produces two main folders (Figure 1):

Sample folder: The sample folder contains sample-specific files regarding contamination.
MultiQC folder

Interpretation - MultiQC

Description for each section of the MultiQC report

This section will guide you in how to interpret the output from running the ACCESS QC workflow. The main output from running the ACCESS QC workflow is a report (for both single sample and multiple samples). Each subsection explains certain parts of the MultiQC report.

Summary QC metrics

Summary of all quality control metrics generated using the workflow

The first section of the MultiQC report is the Summary QC metrics table that displays the summary information per sample. The metrics presented are mainly lab sample quality metrics, alignment information, and quality of the target capture.

Interpretation

In the above table, the coloring represents the QC criteria of the values set by the Bioinformatics tram. The coloring schema is either red, yellow, or green, which indicates if the metric fails, is borderline, or passes the thresholds. This allows the Bioinformatics team to quickly glance at all samples to see where potential issues are. Below are the descriptions for each column and were the data was obtained from.

Coverage vs GC content

Awareness of possible loss of accuracy in downstream sequencing results due to coverage due to GC content bias.

The figure plots below represent the normalized coverage against the % GC content from the CMO-CH target regions. Each line is data from a single sample.

Methods

Tool used: GATK-CollectHsMetrics BAM type: (1) collapsed BAM and (2) uncollapsed BAM.

The data used to produce this figure are the values under the normalized_coverage and %gc columns, which are in the *_per_target_coverage.txt the output file from CollectHsMetrics. For each sample separately, the % GC content for each target region is calculated, followed by binning the target regions by their GC content (in 5% intervals). Then for each bin, the mean coverage is calculated and then normalized across all regions that fall into each GC bin.

Interpretation

Extreme base compositions, i.e., GC-poor or GC-rich sequences, lead to an uneven coverage or even no coverage of reads across the genome. This can affect downstream small variants and copy number calling. Both of these rely on consistent sequencing depth across all regions. Ideally, this plot should be as flat as possible. High GC-rich regions have a decrease in coverage as these regions are harder to sequence.

Capture Metrics

Validating the efficacy of the bait sets.

Introduction

There are several sections displaying bait set capture efficiency. Each section corresponds to a separate BAM type and bait set combination. The tool used to produce the metrics is GATK-CollectHsMetrics. By default, only the mean bait coverage, mean target coverage, and % Usable bases on-target are displayed. However, there are many more metrics that can be toggled to display by clicking on the Configure Columns button.

Methods

Tool used: BAM type: (1) Uncollapsed BAM, (1) Collapsed BAM, (1) Duplex BAM, and (4) Simplex BAM

Interpretation

The aim is to have high coverage across the panel.

Insert Size

Confirmation of fragment length information for different sample types

Introduction

This figure below represents the insert size distribution from the CMO-CH target regions. Insert size is calculated from the start and stop positions of the reads after mapping to the reference genome.

Methods

Tool used: BAM type: Collapsed BAM

The data used to produce this figure are the values under the MODE_INSERT_SIZE column contained in the output file from CollectInsertSizeMetrics.

Interpretation

Usually this plot has a specific shape as Cell free DNA has distinctive features due to the natural processes behind its fragmentation. One such feature is the set of 10-11 bp fluctuations that indicate the preferential splicing of fragments due to the number of bases per turn of the DNA helix, which causes a unique pattern of binding to the surface of histones.

The more pronounced peak at 166 bp indicate complete wrapping of the DNA around the histones' circumference, and similarly the second more pronounced peak indicates two complete wraps.

However in the CMO-CH panel we are using Buffy coat samples. These samples are mechanically sheared and thus do not exhibit these distinctive features, hence the different shape for their distribution in comparison to other reports.

Target coverage distribution

Introduction

This figure shows the density plot of coverage values from the ACCESS target regions. Each line is data from one sample. Each sample is normalized by the median coverage value of that sample to align all peaks with one another and correct for sample-level differences.

Methods

Tool used: BAM type: Collapsed BAM

The data used to produce this figure are the values under the normalized_coverage column, which are in the *_per_target_coverage.txt output file from CollectHsMetrics. Then the gaussian_kde function from the python scipy package is used to produce the density plot.

Interpretation

Each distribution should be unimodal, apart from a second peak on the low end due to X chromosome mapping from male samples. Narrow peaks are indicative of evenly distributed coverage across all bait regions. Wider distributions indicate uneven read distribution and may be correlated with a large GC bias. Note that the provided bed file lists the start and stop coordinates of ACCESS design probes, not the actual genomic target regions.

Duplex Metrics

Duplex family sizes

Understanding the frequency of UMI families of different read counts

We investigate the number of Duplex families by plotting the count of the number of families with the ab and ba single-strand families of size ab_size and ba_size.

Simplex family sizes

We investigate the number of Simplex families by plotting the count of the number of families with the ab and ba single-strand families of size ab_size and ba_size.

Duplex yield metrics

Metrics produced by CollectDuplexSeqMetrics that are sampled at various levels of coverage, via random downsampling, during the construction of duplex metrics. The downsampling is done in such a way that the fractions are approximate, and not exact, therefore the fraction the field should only be interpreted as a guide, and the read_pairs field used to quantify how much data was used.

Mean Base Quality

Introduction

This figure below illustrates the mean base quality by cycle BaseQualityScoreRecalibration (BQSR). The sequencer uses the difference in intensity of the fluorescence of the bases to give an estimate of the quality of the base that has been read. The BQSR tool from GATK recalculates these values based on the empirical error rate of the reads themselves, which is a more accurate estimate of the original quality of the read.

Duplex Noise Metrics

Hotspot in Normals

The table below summarised the variants called in hotspot regions in the normal samples.

Major contamination

Major contamination is calculated by the Collapsed BAM and is calculated using the ratio of heterozygous to homozygous sites.

Minor contamination

Minor contamination is calculated separately for collapsed and duplex BAMs. Minor contamination is calculated using just the homozygous sites.

Fingerprinting

Introduction

This section contains a table showing the samples clustered into groups, where each row in the table corresponds to one sample. The table will show whether your samples are grouping together in unexpected ways, which would indicate sample mislabelling.

Methods

Tool used: BAM type: Collapsed BAM Regions: MSK-ACCESS-v1_0-curatedSNPs.vcfIt is a two step process to produce the table: (1) extract SNP genotypes from each sample using biometrics extract command and (2) perform a pairwise comparison of all samples to determine sample relatedness using the biometrics genotype command. Please see the biometrics documentation for further documentation on the methods.

Interpretation

Below is a description of all the columns.

QC thresholds

QC thresholds are specified in the config file and I

CMO-CH QC thresholds

Metric

PASS

WARNING

FAIL

athena_coverage_report_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/athena_coverage_report_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/athena_coverage_report_dir/C-40R694-N001-d01/
collapsed_bam_duplex_metrics_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_duplex_metrics_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_duplex_metrics_dir/C-40R694-N001-d01
collapsed_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_stats_dir/C-40R694-N001-d01
collapsed_extraction_files:
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/C-JU5J5X-N001-d01/C-JU5J5X-N001-d01_collapsed.pickle
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/C-40R694-N001-d01/C-40R694-N001-d01_collapsed.pickle
config:
  class: File
  path: /work/bergerm1/bergerlab/charalk/projects/nucleo_qc/repos/220825_nucleo_qc/nucleo_qc_generation/multiqc_configs/config_ch.yaml
duplex_bam_sequence_qc_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_sequence_qc_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_sequence_qc_dir/C-40R694-N001-d01
duplex_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_stats_dir/C-40R694-N001-d01
duplex_extraction_files:
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/C-JU5J5X-N001-d01/C-JU5J5X-N001-d01_duplex.pickle
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/C-40R694-N001-d01/C-40R694-N001-d01_duplex.pickle
gatk_mean_quality_by_cycle_recal_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/gatk_mean_quality_by_cycle_recal_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/gatk_mean_quality_by_cycle_recal_dir/C-40R694-N001-d01
samples-json:
  class: File
  path: /work/bergerm1/bergerlab/charalk/projects/nucleo_qc/repos/agg_vis_3167_C/samples_3167_C_sub.json
simplex_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/simplex_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/simplex_bam_stats_dir/C-40R694-N001-d01
uncollapsed_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/uncollapsed_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/uncollapsed_bam_stats_dir/C-40R694-N001-d01
biometrics_extract_files_dir:
- class: Directory
  path: test_data/all_qc_files/biometrics_extract_files_dir/Myeloid200-1-05500HJ_P20/
- class: Directory
  path: test_data/all_qc_files/biometrics_extract_files_dir/Myeloid200-2-05500HJ_P20/y

inputs.yaml

omaf: true
output: null
reference:
  path: /juno/work/cch/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.fasta
  class: File
  secondaryFiles:
    - path: /work/cch/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.fasta.fai
      class: File
    - path: /work/cch/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.dict
      class: File
athena_vcf: null
duplex_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_duplex.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_duplex.bai
        class: File
sample_sex:
  - unknown
sample_name:
  - C-T496P0-N001-d01
simplex_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_simplex.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_simplex.bai
        class: File
athena_build: null
athena_cores: 4
athena_limit: null
hotspots_maf:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/hotspot-list-union-v1-v2_with_TERT.maf
  class: File
mosdepth_bed:
  path: /work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/panel_bed_file_athena_CH_nodup.bed
  class: File
sample_group:
  - C-T496P0
samples-json:
  path: /juno/work/ci/temp/897c0b7d-8631-4e55-8f86-5a435a84b9e1/samples_json.json
  class: File
collapsed_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_FM.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_FM.bai
        class: File
athena_summary: true
bait_intervals:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/picard_baits.interval_list
  class: File
fragment_count: 1
multiqc_config:
  path: /work/cch/production/resources/cmo-ch/versions/v1.0/multiqc_config/versions/v1.0/config_ch.yaml
  class: File
noise_sites_bed:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/picard_baits.bed
  class: File
athena_threshold: 500
filter_duplicate: 0
generic_counting: true
target_intervals:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/picard_baits.interval_list
  class: File
athena_thresholds:
  - 250
  - 500
  - 1000
  - 1500
  - 2000
biometrics_vcf_file:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/fp_tiling_snps.vcf
  class: File
athena_transcript_file: null
group_reads_by_umi_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_grouped.bam
    class: File
uncollapsed_bam_base_recal:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_uncollapsed_BR.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_uncollapsed_BR.bai
        class: File

athena_coverage_report_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/athena_coverage_report_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/athena_coverage_report_dir/C-40R694-N001-d01/
collapsed_bam_duplex_metrics_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_duplex_metrics_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_duplex_metrics_dir/C-40R694-N001-d01
collapsed_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/collapsed_bam_stats_dir/C-40R694-N001-d01
collapsed_extraction_files:
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/C-JU5J5X-N001-d01/C-JU5J5X-N001-d01_collapsed.pickle
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/C-40R694-N001-d01/C-40R694-N001-d01_collapsed.pickle
config:
  class: File
  path: /work/bergerm1/bergerlab/charalk/projects/nucleo_qc/repos/220825_nucleo_qc/nucleo_qc_generation/multiqc_configs/config_ch.yaml
duplex_bam_sequence_qc_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_sequence_qc_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_sequence_qc_dir/C-40R694-N001-d01
duplex_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/duplex_bam_stats_dir/C-40R694-N001-d01
duplex_extraction_files:
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/C-JU5J5X-N001-d01/C-JU5J5X-N001-d01_duplex.pickle
  - class: File
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/C-40R694-N001-d01/C-40R694-N001-d01_duplex.pickle
gatk_mean_quality_by_cycle_recal_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/gatk_mean_quality_by_cycle_recal_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/gatk_mean_quality_by_cycle_recal_dir/C-40R694-N001-d01
samples-json:
  class: File
  path: /work/bergerm1/bergerlab/charalk/projects/nucleo_qc/repos/agg_vis_3167_C/samples_3167_C_sub.json
simplex_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/simplex_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/simplex_bam_stats_dir/C-40R694-N001-d01
uncollapsed_bam_stats_dir:
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/cf19eabf-29da-4448-a42d-d72af47e75b6/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/uncollapsed_bam_stats_dir/C-JU5J5X-N001-d01/
  - class: Directory
    path: /juno/work/access/production/runs/voyager/staging/cmo_ch_qc/90cbad6f-3361-49f2-9ef1-eabcaf90d352/multiqc_1.10.1.7/aggregate_parsed_stats/all_qc_files/uncollapsed_bam_stats_dir/C-40R694-N001-d01
biometrics_extract_files_dir:
- class: Directory
  path: test_data/all_qc_files/biometrics_extract_files_dir/Myeloid200-1-05500HJ_P20/
- class: Directory
  path: test_data/all_qc_files/biometrics_extract_files_dir/Myeloid200-2-05500HJ_P20/y

inputs.yaml

omaf: true
output: null
reference:
  path: /juno/work/cch/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.fasta
  class: File
  secondaryFiles:
    - path: /work/cch/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.fasta.fai
      class: File
    - path: /work/cch/production/resources/reference/versions/hg19/Homo_sapiens_assembly19.dict
      class: File
athena_vcf: null
duplex_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_duplex.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_duplex.bai
        class: File
sample_sex:
  - unknown
sample_name:
  - C-T496P0-N001-d01
simplex_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_simplex.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_simplex.bai
        class: File
athena_build: null
athena_cores: 4
athena_limit: null
hotspots_maf:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/hotspot-list-union-v1-v2_with_TERT.maf
  class: File
mosdepth_bed:
  path: /work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/panel_bed_file_athena_CH_nodup.bed
  class: File
sample_group:
  - C-T496P0
samples-json:
  path: /juno/work/ci/temp/897c0b7d-8631-4e55-8f86-5a435a84b9e1/samples_json.json
  class: File
collapsed_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_FM.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_FM.bai
        class: File
athena_summary: true
bait_intervals:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/picard_baits.interval_list
  class: File
fragment_count: 1
multiqc_config:
  path: /work/cch/production/resources/cmo-ch/versions/v1.0/multiqc_config/versions/v1.0/config_ch.yaml
  class: File
noise_sites_bed:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/picard_baits.bed
  class: File
athena_threshold: 500
filter_duplicate: 0
generic_counting: true
target_intervals:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/picard_baits.interval_list
  class: File
athena_thresholds:
  - 250
  - 500
  - 1000
  - 1500
  - 2000
biometrics_vcf_file:
  path: /juno/work/cch/production/resources/cmo-ch/versions/v1.0/regions_of_interest/versions/v1.0/fp_tiling_snps.vcf
  class: File
athena_transcript_file: null
group_reads_by_umi_bam:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_collapsed_grouped.bam
    class: File
uncollapsed_bam_base_recal:
  - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_uncollapsed_BR.bam
    class: File
    secondaryFiles:
      - path: /juno/work/access/production/runs/voyager/staging/cmo_ch_nucelo/07cc97f0-c83b-41a2-a308-debdd6404968/C-T496P0-N001-d01_uncollapsed_BR.bai
        class: File

Nucleo Quality Control

hashtagIntroduction

hashtagCredits

Workflow description

Requirements

hashtagBefore installing the pipeline, make sure your system supports these requirements

Installation and Usage

hashtagStep 1: Create a virtual environment.

hashtagOption (A) - if using cwltool

Workflow inputs

hashtagParameter Used by Tools

hashtagCommon Parameters Across Tools

Input for nucleo_qc.cwl

hashtagOption 1: Input.yml example to run workflow enable mosdepth/athena to create coverage reports

hashtag

Input for nucleo_aggregate_visualize.cwl

Workflow outputs

Interpretation - MultiQC

hashtagTable of Contents

Summary QC metrics

hashtagInterpretation

Coverage vs GC content

hashtagMethods

hashtagInterpretation

Capture Metrics

hashtagIntroduction

hashtagMethods

hashtagInterpretation

Insert Size

hashtagIntroduction

hashtagMethods

hashtagInterpretation

Target coverage distribution

hashtagIntroduction

hashtagMethods

hashtagInterpretation

Duplex Metrics

Duplex family sizes

Simplex family sizes

Duplex yield metrics

Mean Base Quality

hashtagIntroduction

Duplex Noise Metrics

Hotspot in Normals

Major contamination

Minor contamination

Fingerprinting

hashtagIntroduction

hashtagMethods

hashtagInterpretation

QC thresholds

hashtagCMO-CH QC thresholds

Nucleo Quality Control

hashtagIntroduction

hashtagCredits

Major contamination

Workflow description

QC thresholds

hashtagCMO-CH QC thresholds

Fingerprinting

hashtagIntroduction

hashtagMethods

hashtagInterpretation

Workflow inputs

hashtagParameter Used by Tools

hashtagCommon Parameters Across Tools

Installation and Usage

hashtagStep 1: Create a virtual environment.

hashtagOption (A) - if using cwltool

Workflow outputs

Input for nucleo_aggregate_visualize.cwl

Input for nucleo_qc.cwl

hashtagOption 1: Input.yml example to run workflow enable mosdepth/athena to create coverage reports

hashtag

Requirements

hashtagBefore installing the pipeline, make sure your system supports these requirements

Summary QC metrics

hashtagInterpretation

Interpretation - MultiQC

hashtagTable of Contents

Introduction

Credits

Before installing the pipeline, make sure your system supports these requirements

Step 1: Create a virtual environment.

Option (A) - if using cwltool

Parameter Used by Tools

Common Parameters Across Tools

Option 1: Input.yml example to run workflow enable mosdepth/athena to create coverage reports

Table of Contents

Interpretation

Methods

Interpretation

Introduction

Methods

Interpretation

Introduction

Methods

Interpretation

Introduction

Methods

Interpretation

Introduction

Introduction

Methods

Interpretation

CMO-CH QC thresholds

Introduction

Credits

CMO-CH QC thresholds

Introduction

Methods

Interpretation

Parameter Used by Tools

Common Parameters Across Tools

Step 1: Create a virtual environment.

Option (A) - if using cwltool

Option 1: Input.yml example to run workflow enable mosdepth/athena to create coverage reports

Before installing the pipeline, make sure your system supports these requirements

Interpretation

Table of Contents

Option (B) - recommended for Juno HPC cluster

Step 2: Clone the repository

Step 3: Install requirements using pip

Step 4: Load singularity and nodejs for HPC

Step 5: Generate an inputs file

Step 5: Run the workflow

Option A:

Run the workflow with a given set of input using cwltool on single machine

Run the workflow with a given set of input using on single machine

Option B:

Introduction

Methods

Interpretation

Introduction

Methods

Interpretation

Introduction

Methods

Interpretation

Methods

Interpretation

Introduction

Interpretation

Introduction