98296985b0763ebf2d6add3b51d9200ac6940d77 abenetpa Thu Nov 5 06:21:39 2020 -0800 added variant regions in track description refs #24349 diff --git src/hg/makeDb/trackDb/human/giab.html src/hg/makeDb/trackDb/human/giab.html index 418b72c..ca9f5a4 100644 --- src/hg/makeDb/trackDb/human/giab.html +++ src/hg/makeDb/trackDb/human/giab.html @@ -5,33 +5,33 @@ Bottle Consortium (GIAB)</b></a>, an open, public consortium hosted by <a target="_blank" href="https://www.nist.gov/">NIST</a>. The priority of GIAB is to develop reference standards, reference methods, and reference data by authoritative characterization of human genomes for use in <b>benchmarking</b>, including analytical validation and technology development that will support translation of whole human genome sequencing to clinical practice. The sole purpose of this work is to provide validated variants and regions to enable technology and bioinformatics developers to benchmark and optimize their detection methods. </p> <p> The <b>Ashkenazim and the Chinese Trio tracks</b> show benchmark <b>SNV calls</b> from two son/father/mother trios of Ashkenazi Jewish and Han Chinese ancestry from the <a target="_blank" href="https://www.personalgenomes.org/us">Personal Genome Project</a>, consented for commercial redistribution. </p> <p> -The <b>Genome In a Bottle Structural Variants track</b> shows benchmark <b>SV calls</b> (5,262 -insertions and 4,095 deletions, > 50 bp, in 2.51 Gb of the genome) from the son (HG002/NA24385) -from the Ashkenazi Jewish trio. +The <b>Genome In a Bottle Structural Variants track</b> shows benchmark <b>SV calls</b> (nssv) +and <b>variant regions</b> (nsv) (5,262 insertions and 4,095 deletions, > 50 bp, in 2.51 Gb of +the genome) from the son (HG002/NA24385) from the Ashkenazi Jewish trio. </p> <p> Samples are disseminated as National Institute of Standards and Technology (NIST) <a target="_blank" href="https://www.coriell.org/1/NIGMS/Collections/NIST-Reference-Materials">Reference Materials</a>. </p> <h2>Display Conventions and Configuration</h2> These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described <a target="_blank" href="../goldenPath/help/multiView.html">here</a>. </p> <p> Unlike a regular genome browser track, the <b>Ashkenazim and the Chinese Trio</b> tracks display the genome variants of each individual as two <b>haplotypes</b>; SNPs, small insertions and deletions are mapped to each haplotype based on the <b>phasing</b> information of the VCF file. The