85320722a5537e851769a87a141b2094aa145847 max Mon Oct 5 01:29:25 2026 -0700 phasedVars.html: comment out the hgdp1kSnv methods paragraph until that subtrack is released, refs #37306 diff --git src/hg/makeDb/trackDb/human/phasedVars.html src/hg/makeDb/trackDb/human/phasedVars.html index 80f7a4496df..05d52541dcb 100644 --- src/hg/makeDb/trackDb/human/phasedVars.html +++ src/hg/makeDb/trackDb/human/phasedVars.html @@ -95,42 +95,44 @@ <p> <b>MXB:</b> Allele frequencies by geographical state and ancestry are available via the <a target="_blank" href="https://morenolab.shinyapps.io/mexvar/">MexVar platform</a>. Raw genotype data are available under controlled access at the EGA (Study: EGAS00001005797; Dataset: EGAD00010002361). For the VCFs, email andres.moreno@cinvestav.mx. </p> <h2>Methods</h2> <p> <b>SGDP:</b> The version used was <a target="_blank" href="https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/" >https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/</a>, merged with bcftools and lifted to hg38 with CrossMap. </p> +<!-- hgdp1kSnv is release alpha: uncomment this paragraph when it is released, refs #37306 <p> <b>gnomAD HGDP+1000G, SNVs AC>5:</b> The full gnomAD callset is 3.5 TB and too slow to display in haplotype clustering mode except in very small windows. For this second, smaller version we kept only single-nucleotide variants with an allele count (INFO/AC) higher than five, only the GT genotype field and only the AC, AN and AF INFO fields, using bcftools. Indels, rare variants and all other fields are only in the full track. See the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc</a> and the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs/hgdp1kCommonSnvs.sh" target="_blank">script</a> for details. </p> +--> <h2>Credits</h2> <p> <b>MXB:</b> We thank the Center for Research and Advanced Studies (Cinvestav) of Mexico for generating and providing the frequency data, the National Institute of Medical Sciences and Nutrition (INCMNSZ) for DNA extraction, and the Ministry of Health together with the National Institute of Public Health (INSP) for the design and implementation of the National Health Survey 2000 (ENSA 2000). We also thank the ENSA-Genomics Consortium for their contributions to sample collection and data processing that made possible the construction of the MXB genomic resource. </p> <p> <b>SGDP:</b> This project was funded by the Simons Foundation. Thanks to David Reich and Swapan Mallick for help with importing the data.