benchmarks:
  giab-na12878-exome:
    genome: na12878
    bam-url: ftp://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Nebraska_NA12878_HG001_TruSeq_Exome/NIST-hg001-7001-ready.bam
    target-regions: ftp://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Nebraska_NA12878_HG001_TruSeq_Exome/TruSeq_exome_targeted_regions.hg19.bed
    grch37: true
    high-coverage: false

  chm-eval:
    genome: chm-eval
    bam-url: ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR134/ERR1341796/CHM1_CHM13_2.bam
    grch37: false
    high-coverage: false

  seqc2-wes:
    genome: seqc2-somatic
    bam-url: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/WES/WES_EA_T_1.bwa.dedup.bam
    target-regions: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/technical/reference_genome/Exome_Target_bed/S07604624_Covered_human_all_v6_plus_UTR.liftover.to.hg38.bed6.gz
    grch37: false
    vaf-field:
      field: INFO # either FORMAT or INFO
      name: TVAF # name of tumor variant allele frequency
    high-coverage: true

  seqc2-wgs:
    genome: seqc2-somatic
    bam-url: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/WGS/WGS_NS_T_1.bwa.dedup.bam
    grch37: false
    vaf-field:
      field: INFO # either FORMAT or INFO
      name: TVAF # name of tumor variant allele frequency
    high-coverage: false

  seqc2-ffpe:
    genome: seqc2-somatic
    bam-url: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/FFX/FFX_IL_T_24h_1.bwa.dedup.bam
    target-regions: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/technical/reference_genome/Exome_Target_bed/S07604624_Covered_human_all_v6_plus_UTR.liftover.to.hg38.bed6.gz
    grch37: false
    vaf-field:
      field: INFO # either FORMAT or INFO
      name: TVAF # name of tumor variant allele frequency
    high-coverage: true

  imgag-5:
    genome: na12878-somatic
    bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_5.bam
    target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed
    grch37: false
    high-coverage: true

  imgag-10:
    genome: na12878-somatic
    bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_10.bam
    target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed
    grch37: false
    high-coverage: true

  imgag-20:
    genome: na12878-somatic
    bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_20.bam
    target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed
    grch37: false
    high-coverage: true

  imgag-40:
    genome: na12878-somatic
    bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_40.bam
    target-regions: https://download.imgag.de/public/validation_dataset_somatic/Twist_Custom_Exome_IMGAG_v2.bed
    grch37: false
    high-coverage: true

genomes:
  na12878:
    version: 4.2.1
    truth:
      grch37: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh37/HG001_GRCh37_1_22_v4.2.1_benchmark.vcf.gz
      grch38: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
    confidence-regions:
      grch37: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh37/HG001_GRCh37_1_22_v4.2.1_benchmark.bed
      grch38: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed

  chm-eval:
    version: 0.5
    archive: https://github.com/lh3/CHM-eval/releases/download/v0.5/CHM-evalkit-20180222.tar
    truth:
      grch38: full.38.vcf.gz
      grch37: full.37m.vcf.gz
    confidence-regions:
      grch38: full.38.bed.gz
      grch37: full.37m.bed.gz

  seqc2-somatic:
    version: 1.2
    truth:
      grch38:
        snvs: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/high-confidence_sSNV_in_HC_regions_v1.2.vcf.gz
        indels: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/high-confidence_sINDEL_in_HC_regions_v1.2.vcf.gz
    confidence-regions:
      grch38: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/High-Confidence_Regions_v1.2.bed
    somatic: true

  na12878-somatic:
    version: 4.2.1
    truth:
      grch38: https://zenodo.org/records/15120550/files/NA12878.unique.vcf.gz?download=1
    confidence-regions:
      grch38: https://download.imgag.de/public/validation_dataset_somatic/benchmark_region.bed
    somatic: true