SEQC2 Somatic Mutation Reference Call Set
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Citations for SEQC2
The SEQC2 somatic mutation reference call set is developed and maintained by the SEQC2 Somatic Mutation Working Group. For citation guidance and further information, please refer to the official SEQC2 website at https://sites.google.com/view/seqc2.
Overview
The Sequencing Quality Control Phase 2 (SEQC2) somatic mutation reference call set is a benchmark resource designed to evaluate tumor-normal somatic variant calling workflows. It provides a curated set of somatic mutation calls and corresponding genomic regions where variant detection can be assessed with high confidence.
The v1.2 release incorporates evidence from various sources:
Short-read sequencing
Ensemble calling
NeuSomatic analysis
Deep sequencing
Manual review
New in v1.2: PacBio long-read evidence
For more details, please check the v1.2 release note.
Resource Description
From SEQC2 download source, the resource includes:
VCF Files:
High-Confidence VCFs: Contain only the confidently resolved somatic mutation calls intended for use as truth sets.
high-confidence_sSNV_in_HC_regions_v1.2.vcf.gz..
high-confidence_sINDEL_in_HC_regions_v1.2.vcf.gz.
Updated v1.2.1 High-Confidence VCFs: The v1.2.1 files were generated by intersecting the original v1.2 high-confidence VCFs with the official High-Confidence_Regions_v1.2.bed file. This update ensures that all variants included in the v1.2.1 VCF files fall within the defined high-confidence regions. Check this official README file for more information.
high-confidence_sSNV_in_HC_regions_v1.2.1.vcf.gz.
high-confidence_sINDEL_in_HC_regions_v1.2.1.vcf.gz.
All-Inclusive Super Set VCFs: Provide a broader set of candidate calls with varying confidence levels.
sSNV.MSDUKT.superSet.v1.2.vcf.gz.
sINDEL.MDKT.superSet.v1.2.vcf.gz.
BED File (High-Confidence Regions): This file contains the regions of the genome where somatic mutations could be confidently determined. It excludes uncallable and unresolved genome regions. Variant calls outside these regions could not be confidently resolved.
High-Confidence_Regions_v1.2.bed.
Genotype Addition from nf-core/variantbenchmarking
The original SEQC2 VCF files do not contain a FORMAT or sample column, which is required by standard benchmarking tools. A heterozygous genotype value (GT 0/1) was added to each variant to enable compatibility. Modified files with genotype information are available in the SEQC2/ folder on the DNAnexus platform. Please refer to the nf-core/variantbenchmarking user guide for further details on this modification.
SEQC2 on the DNAnexus platform
Benchmark VCF and BED files for the SEQC2 somatic mutation reference call set are publicly available from the NCBI ReferenceSamples SEQC release directory.
Accessing SEQC2 data on the DNAnexus platform
The SEQC2 truth datasets are pre-staged in the Public Datasets AWS US East project and can be accessed directly without copying. To use the files in your own project, you can copy them from the public project:
Create a new project billed to your organization. See Setting Up a Project for instructions.
Go to the Resources tab and find the project "Public Datasets AWS US East". Navigate to the SEQC2/ folder.
Select the folders and files you need.
Click Copy from the top right menu and select the project you created in Step 1.
Go to your project to start using the data.
Using SEQC2 data with nf-core/variantbenchmarking
The SEQC2 truth sets available on the DNAnexus platform can be used as input to nf-core/variantbenchmarking via the --truth_vcf, --truth_id, and --regions_bed parameters. Please refer to the nf-core/variantbenchmarking user guide for instructions on how to configure and run the pipeline with these truth sets.
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