NIST GiaB Trios

GIAB high-confidence small variant and reference calls v3.3.2 (6mar)

• GRCh37/38 ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/
• https://docs.google.com/document/d/13XTVwrlAgugYEYtL3W64KX2hy-7xzWNTj8qPN8rULVU/edit?usp=sharing
  • Have Illumina paired-end, mate-pair, Ion, SOLiD, and 10X on haplotypes
  • Aligned with novoalign, variants called using HaplotypeCaller and FreeBayes
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study

• two Personal Genome Project trios of Ashkenazim Jewish and Han Chinese ancestries
• 12 technologies, bio nano, CG, Proton, nanopore, pacbio, solid, 10x genomics, illumina exome & wgs paired-end, mate-pair, synthetic long reads
• 300x coverage of AJ trio, NA12878, and HC son. 100x HC parents.
• Illumina paired-end WGS
  • AJ Trio bams, vcfs, fastqs for HG002, HG003, and HG004, and their gatk/hc joint vcfs
  • NIST suggests the following consensus vcfs for the AJ trio HG002, HG003, and HG004:
  • Chinese son bams and fastqs, father, and mother
  • GemCode bams and vcfs for son, father, mother
  • Other data types available in the article
• GiaB consortium Analysis Team results
  • assembly, small variant calling, structural variant calling, and phasing
  • AJ trio, HC trio, NA12878
  • filename format: analyzer’s name, technology used, variant characterized, analysis tool or algorithm, submission date

NIST github repo - contains announcements, releases, publications, data, tools

precisionfda results are being suggested by NIST as the current gold standard

According to here: "The truth data files have been published on precisionFDA by Dr. Justin Zook (scientist at the National Institute of Standards and Technology and co-leader of the Genome in a Bottle Consortium efforts) ... " then links to here, which says "high-confidence SNP, small indel, and homozygous reference calls for the Genome in a Bottle (GIAB) sample HG001 (aka NA12878), HG002/HG003/HG004 (aka AJ son/father/mother), or HG005 (aka Chinese son) " are available here, which is the same resource NIST GiaB links to. So the precisionFDA results are the ones being suggested by NIST as the gold standard.