nf-core/variantbenchmarking: Truth files

Defining Truth VCF and High confidence BED files

This pipeline requires a set of Truth VCF, as a baseline for comparisons, and a high confidence bed files, to restrict analysis to regions. Although, those sets can be anything depending on the type of the analysis, for benchmarking of human genomes there are golden set of samples provided by Genome in a Bottle project and SEQC2 consortium. Another somatic benchmarking analysis for COLO829 cell line can be found under epi2me project.

Below, please find some set truths can be used for analysis:

params.analysis == 'germline'

params.genome == 'GRCh38'

params.vartype == 'small'

          truth_id          = "HG001"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed"

          truth_id          = "HG002"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"

          truth_id          = "HG003"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"

          truth_id          = "HG004"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh38/HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh38/HG004_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"

          truth_id          = "HG005"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh38/HG005_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh38/HG005_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi"

          truth_id          = "HG006"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv4.2.1/GRCh38/HG006_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv4.2.1/GRCh38/HG006_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi"

          truth_id          = "HG007"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv4.2.1/GRCh38/HG007_GRCh38_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv4.2.1/GRCh38/HG007_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi"

params.vartype == 'structural'

          truth_id          = "HG002_CMRG"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.bed"

params.genome == 'GRCh37'

params.vartype == 'small'

          truth_id          = "HG001"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh37/HG001_GRCh37_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh37/HG001_GRCh37_1_22_v4.2.1_benchmark.bed"

          truth_id          = "HG002"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh37/SupplementaryFiles/HG002_GRCh37_1_22_v4.2.1_highconf.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh37/SupplementaryFiles/HG002_GRCh37_1_22_v4.2.1_highconf.bed"

          truth_id          = "HG003"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh37/HG003_GRCh37_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh37/HG003_GRCh37_1_22_v4.2.1_benchmark_noinconsistent.bed"

          truth_id          = "HG004"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh37/HG004_GRCh37_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh37/HG004_GRCh37_1_22_v4.2.1_benchmark_noinconsistent.bed"

          truth_id          = "HG005"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh37/HG005_GRCh37_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh37/HG005_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi"

          truth_id          = "HG006"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv4.2.1/GRCh37/HG006_GRCh37_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG006_NA24694_father/NISTv4.2.1/GRCh37/HG006_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi"

          truth_id          = "HG007"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv4.2.1/GRCh37/HG007_GRCh37_1_22_v4.2.1_benchmark.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG007_NA24695_mother/NISTv4.2.1/GRCh37/HG007_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi"

params.vartype == 'structural'

          truth_id          = "HG002"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NIST_SV_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NIST_SV_v0.6/HG002_SVs_Tier1_v0.6.bed"

          truth_id          = "HG002_CMRG"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh37/StructuralVariant/HG002_GRCh37_CMRG_SV_v1.00.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh37/StructuralVariant/HG002_GRCh37_CMRG_SV_v1.00.bed"

params.analysis == 'somatic'

params.genome == 'GRCh38'

params.vartype == 'structural'

          truth_id          = "HG002"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.bed"

params.vartype == 'snv'

          truth_id          = "SEQC2"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/high-confidence_sSNV_in_HC_regions_v1.2.1.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/High-Confidence_Regions_v1.2.bed"

params.vartype == 'indel'

          truth_id          = "SEQC2"
          truth_vcf         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/high-confidence_sINDEL_in_HC_regions_v1.2.1.vcf.gz"
          regions_bed       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/High-Confidence_Regions_v1.2.bed"

params.genome == 'GRCh37'
- params.vartype == 'structural' // zenado records available: https://zenodo.org/records/7515830 truth_id = "COLO829" truth_vcf = "https://github.com/UMCUGenetics/COLO829_somaticSV/blob/master/truthset_somaticSVs_COLO829.vcf"

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Defining Truth VCF and High confidence BED files

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nf-core/variantbenchmarking: Truth files

Defining Truth VCF and High confidence BED files