MYE_1.2.7

Updated to include:

Latest ClinVar B38 annotation resource files (20240107)

• clinvar_20240107_hg38_withchr.vcf.gz (file-GfXQZPQ42VYYz4FFqGb0XzQb)

• clinvar_20240107_hg38_withchr.vcf.gz.tbi (file-GfXQZg042VYbPF1vypjbq4zp)

README.md updated to reference correct versions

Detail testing https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3074490380/eggd+conductor+uranus+MYE+config+v1.2.7

CEN_v2.0.0

CEN conductor config for the transition to performing variant calling in GRCh38.
All reference related input files. New files listed below:

["file-GZYqkkQ4fPQpKYz0BYPZk68j","GCF_000001405.39_GRCh38.p13_genomic.exon_5bp.tsv"]
["file-Gb76f204XGybZ3J6F731xkBp","GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18_noChr.bwa-index.tar.gz"]
["file-F3zvKp84fXX8qJx43zZXP395","GRCh38.gatk.resource.bundle.tar.gz"]
["file-G7YKFZj4kj47GxgQ2bKGYV1g","Omni25_genotypes_1525_samples_v2.b38.PASS.ALL.sites_no_chr.vcf.gz"]
["file-Gb772VQ4XGyzQ0Zk615XbZ0X","GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18_noChr.fasta-index.tar.gz"]
["file-Gb757784XGyY3FPvkPQ74K9z","GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18_noChr.fasta.gz"]
["file-GP2bGp848QggjG456FJ1vG95","CEN_regions_captured_grch38_v1.0.0.bed"]
["file-GYv4kJj43bPFv25JX1ZP7Z39","HG001_GRCh38_1_22_v4.2.1_benchmark_noChr.bed"]
["file-GYv4kKQ43bP9XZZXz7bYJJjx","HG001_GRCh38_1_22_v4.2.1_benchmark_noChr.vcf.gz"]
["file-G7FJjz04kj424vq826gKbZx7","sites.hg38.nochr.vcf"]
["file-Gf0265j4XGyVZgV9VkG615xf","CEN_genes_b38_v1.0.0.bed"]
["file-Gb75X184XGypG6k0fq8P6Y6Z","GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18_noChr.sdf.tar"]

Detail for testing https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3064692738/eggd+conductor+dias+CEN+config+v2.0.0.json

MYE_v1.2.6

Updated to include:

Updated Myeloid NovaSeq samples MAF files:

• haemonc_1706_samples.vcf.gz (file-GZJFvq043bFzkk3xBxY6GZyX)

• haemonc_1706_samples.vcf.gz.tbi (file-GZJFvq043bFyG614g32P3K59)

README.md updated to reference correct versions

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3059154945/eggd+conductor+uranus+MYE+config+v1.2.6

MYE_v1.2.5

Updated to include:

Latest ClinVar hg38 annotation resource files (20231217):

• clinvar_20231217_hg38_withchr.vcf.gz (file-Gf03jZj42VYZy6kzQ895pFQf)
• clinvar_20231217_hg38_withchr.vcf.gz.tbi (file-Gf03kZ042VYz0Gz1496XQgj6)

Latest COSMIC hg38 annotation resource files (v99):

• CosmicCodingMuts_GRCh38_v99.normal.vcf.gz (file-Gf02Fxj4Pj2vPPV0zyfpbFkz)
• CosmicCodingMuts_GRCh38_v99.normal.vcf.gz.tbi (file-Gf02JgQ4Pj2xZg2b1g9pVV7g)
• CosmicNonCodingVariants_GRCh38_v99.normal.vcf.gz (file-Gf02Jj04Pj2ZPxF97V6YJFKv)
• CosmicNonCodingVariants_GRCh38_v99.normal.vcf.gz.tbi (file-Gf02KG84Pj2QB86kK721B9yQ)

README.md updated to reference correct versions

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/3056730113/eggd+conductor+uranus+MYE+config+v1.2.5

TSO500 v1.1.0

Summary

Update of eggd_TSO500 from v1.2.0 -> v2.0.0

Release file: assay_configs/TSO500/eggd_conductor_helios_TSO500_config_v1.1.0.json

MYE_v1.2.4

Updated to include:

• Latest ClinVar hg38 annotation resource files (20231112):
  • clinvar_20231112_b38_withchr.vcf.gz.tbi (file-GbJg4b842VYj0XxxV5X0jJz7)
  • clinvar_20231112_b38_withchr.vcf.gz (file-GbJg4Y842VYxBpX7qVYp9j4Y)
• README.md updated to reference correct versions

MYE_v1.2.3

Updated to include:

• Latest COSMIC annotation resource files (v98):

  • CosmicNonCodingVariants_GRCh38_v98.normal.vcf.gz.tbi (file-GVgVpb8436pPYJv6BzKZ7vq3)
  • CosmicNonCodingVariants_GRCh38_v98.normal.vcf.gz (file-GVgVpb8436p31GYkx142xgPv)
  • CosmicCodingMuts_GRCh38_v98.normal.vcf.gz (file-GVgVpb8436p717kp00bz8Jy5)
  • CosmicCodingMuts_GRCh38_v98.normal.vcf.gz.tbi (file-GVgVpb8436p66kV0VpJp9bYK)

• Latest ClinVar B38 annotation resource files (20231015)

  • clinvar_20231015_b38_withchr.vcf.gz.tbi (file-GZg4jgQ42VYbV4zZkVk02Vy0)
  • clinvar_20231015_b38_withchr.vcf.gz (file-GZg4jJQ42VYpq8g3Y8Fgf1Kg)

• README.md updated to reference correct versions

CEN_v1.2.0

Summary:

• Update the CEN assay config file to use the mem2_ssd1_v2_x8 instance type for MultiQC

Confluence page: https://cuhbioinformatics.atlassian.net/wiki/spaces/DV/pages/2995355684/eggd+conductor+dias+CEN+config+v1.2.0.json

TWE v1.1.1 & CEN v1.1.1

both configs updated to use project-F3zxk7Q4F30Xp8fG69K1Vppj and project-F3zqGV04fXX5j7566869fjFq instead of project-Fv2gqv04kxV0QZgY3gZ1VG0P for somalier genome references

target files:
/assay_configs/CEN/eggd_conductor_dias_CEN_config_v1.1.1.json
/assay_configs/TWE/eggd_conductor_dias_TWE_config_v1.1.1.json

MYE_v1.2.1

Summary:

• Update to MYE assay config file to add updated Epic procedure code in the assay_code field

Release file: /assay_configs/MYE/eggd_conductor_uranus_MYE_config_v1.2.1.json