986c4ede954e44904eb314772fb2cf83a48d307c max Wed May 6 06:24:47 2026 -0700 varFreqs: lift GenomeAsia (gasp + gaspIndel) GRCh37 -> hg38 Both subtracks were served at /gbdb/hg38/ but the upstream callset is GRCh37 (caught in QA, see #36642 note 2026-05-04). Lifted with CrossMap using hg19ToHg38.over.chain.gz; recipe matches tishkoff180 / mxbFreq. gasp (SNVs): 66,236,516 -> 66,222,771 (99.98%; 6,240 unmapped + 7,505 alt/random) gaspIndel: 4,415,156 -> 4,410,871 (99.90%; 3,332 unmapped + 953 alt/random) New driver script: scripts/varFreqs/gaspLift.sh. gaspIndel bigDataUrl renamed from All.indels.annot.cont_withmaf.vcf.gz to ga100k.indels.vcf.gz (old name was a verbatim copy of the upstream download name). varFreqsAll combined bigBed regenerated to fold in the corrected coordinates (36.5 GB, 1,166,451,644 items, 125 fields). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/gasp.html src/hg/makeDb/trackDb/human/gasp.html index 8efa4f255bb..09e43208d44 100644 --- src/hg/makeDb/trackDb/human/gasp.html +++ src/hg/makeDb/trackDb/human/gasp.html @@ -1,50 +1,56 @@ <h2>Description</h2> <p> The <a href="https://www.genomeasia100k.org/" target="_blank">GenomeAsia 100K</a> project aims to sequence 100,000 Asian individuals. This pilot release (GAsP) contains whole-genome sequencing data of 1,739 individuals from 219 population groups across Asia. Frequencies are broken down by Northeast Asian, Southeast Asian, and South Asian ancestry groups. The data is split into two subtracks: substitutions and indels. </p> <h2>Data Access</h2> <p> The data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, our <a href="https://api.genome.ucsc.edu">REST API</a> can be used; the track name is <em>gasp</em>. For bulk download, the VCF file can be obtained from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/" target="_blank">our download server</a>. </p> <p> The original VCFs are also available from the <a href="https://browser.genomeasia100k.org/#tid=download" target="_blank">GenomeAsia 100K website</a>. No license nor login is required. </p> <h2>Methods</h2> <p> Samples were sequenced on Illumina HiSeq 2500, HiSeq 4000, and HiSeq X Ten instruments with 2×100 bp or 2×150 bp paired-end reads at an average depth of 36x. Reads were aligned to GRCh37 using BWA-MEM. Duplicate reads were marked with SAMBLASTER and sorted with Sambamba. Per-sample variant calling was performed with GATK HaplotypeCaller in GVCF mode, followed by joint genotyping with GenotypeGVCFs. Variant quality score recalibration (VQSR) was applied at a 99% sensitivity tranche for both SNPs and indels. Sample-level QC included contamination checks with verifyBamID and sex concordance verification. The final callset contains ∼65 million variants across 1,739 individuals from 219 populations. </p> <p> +The upstream callset is on GRCh37. We lifted it to hg38 using +<a href="https://crossmap.sourceforge.net/" target="_blank">CrossMap</a> and the UCSC +<tt>hg19ToHg38</tt> chain file. After lifting, variants that landed on alt, random, fix, or +unplaced contigs were dropped, and the result was sorted and indexed with tabix. +</p> +<p> We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track. For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>. </p> <h2>References</h2> <p> GenomeAsia100K Consortium. <a href="https://doi.org/10.1038/s41586-019-1793-z" target="_blank"> The GenomeAsia 100K Project enables genetic discoveries across Asia</a>. <em>Nature</em>. 2019 Dec;576(7785):106-111. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31802016" target="_blank">31802016</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054211/" target="_blank">PMC7054211</a> </p>