0bcf60137c26f30375bb9f03edd6da8354fdf26c jnavarr5 Fri Oct 23 16:53:34 2020 -0700 Making each line less than 100 characters. Updated a link to the multi-view docs to use the relative path. refs #24349 #25873 diff --git src/hg/makeDb/trackDb/human/giab.html src/hg/makeDb/trackDb/human/giab.html index 0f0676a..418b72c 100644 --- src/hg/makeDb/trackDb/human/giab.html +++ src/hg/makeDb/trackDb/human/giab.html @@ -1,71 +1,73 @@ <h2>Description</h2> <p> The tracks listed here contain data from -<a target="_blank" href="https://www.nist.gov/programs-projects/genome-bottle"><b>The Genome in a Bottle Consortium (GIAB)</b></a>, -an open, public consortium hosted by +<a target="_blank" href="https://www.nist.gov/programs-projects/genome-bottle"><b>The Genome in a +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 +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. -<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. </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>. +<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="https://genome.ucsc.edu/goldenPath/help/multiView.html">here</a>. +<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 <em>haplotype</em> -1 and the <em>haplotype 2</em> are displayed as two separate black lanes for the browser window -region. Each variant is drawn as a vertical dash. <b>Homozygous variants</b> will show two identical -dashes on both haplotype lanes. <b>Phased heterozygous variants</b> are placed on one of the haplotype -lanes and <b>unphased heterozygous variants</b> are displayed in the area between the two haplotype lanes. +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 +<em>haplotype</em> 1 and the <em>haplotype 2</em> are displayed as two separate black lanes for the +browser window region. Each variant is drawn as a vertical dash. <b>Homozygous variants</b> will +show two identical dashes on both haplotype lanes. <b>Phased heterozygous variants</b> are placed on +one of the haplotype lanes and <b>unphased heterozygous variants</b> are displayed in the area +between the two haplotype lanes. </p> <p> Predicted de novo variants and variants that are inconsistent with phasing in the trio son can be colored in <b><font color="red">red</font></b> using the track Configuration options. </p> <h2>Data Access</h2> The raw data can be explored interactively with the <a target="_blank" href="../cgi-bin/hgTables"> Table Browser</a>, or the <a target="_blank" href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a target="_blank" href="/goldenPath/help/api.html">REST API</a>. </p> <p> Benchmark VCF and BED files for small variants are available for GRCh37 and GRCh38 under each -genome at <a target="_blank" href="ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/">NCBI FTP</a> site. +genome at <a target="_blank" +href="ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/">NCBI FTP</a> site. Structural variants are available for GRCh37 at dbVAR <a target="_blank" href+"https://www.ncbi.nlm.nih.gov/sites/dbvarapp/studies/nstd175/">nst175</a>. </p> <h2>References</h2> <p> Zook JM, McDaniel J, Olson ND, Wagner J, Parikh H, Heaton H, Irvine SA, Trigg L, Truty R, McLean CY <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/30936564" target="_blank"> An open resource for accurately benchmarking small variant and reference calls</a>. <em>Nat Biotechnol</em>. 2019 May;37(5):561-566. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30936564" target="_blank">30936564</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500473/" target="_blank">PMC6500473</a> </p>