d2a02f56a0e84d51213d44955b694ce7daace230 jnavarr5 Fri May 31 11:41:50 2019 -0700 Updating redirected links for hg18, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/hgdpGeo.html src/hg/makeDb/trackDb/human/hgdpGeo.html index c1428e5..8acb96e 100644 --- src/hg/makeDb/trackDb/human/hgdpGeo.html +++ src/hg/makeDb/trackDb/human/hgdpGeo.html @@ -1,70 +1,70 @@ <H2>Description</H2> <P> This track shows the 657,000 SNPs genotyped in 53 populations worldwide by the <a href="http://www.hagsc.org/hgdp/" target="_blank">Human Genome Diversity Project</a> in collaboration with the <a href="http://www.cephb.fr/en/hgdp_panel.php" target="_blank">Centre d'Etude du Polymorphisme Humain</a> (HGDP-CEPH). This track and several others are available from the <A HREF="http://hgdp.uchicago.edu/" TARGET=_BLANK>HGDP Selection Browser</A>. </P> <H2>Methods</H2> <P> Samples collected by the HGDP-CEPH from 1,043 individuals from around the world were genotyped for 657,000 SNPs at <a href="http://www.hagsc.org/hgdp/" target="_blank">Stanford</a>. Ancestral states for all SNPs were estimated using whole genome human-chimpanzee alignments from the UCSC database. For each SNP in the human genome (NCBI Build 35, UCSC database hg17), the allele at the corresponding position in the chimp genome (Build 2 version 1, UCSC database pantro2) was used as ancestral. </P> <P> Allele frequencies were plotted on a world map using programs included in the <A HREF="http://gmt.soest.hawaii.edu/" TARGET=_BLANK>Generic Mapping Tools</A>. </P> <H2>Credits</H2> <P> Thanks to the HGDP-CEPH, the <a href="http://web.stanford.edu/group/pritchardlab/home.html" target="_blank">Pritchard lab</a> at Stanford University, Joe Pickrell and John Novembre for sharing the data and plotting scripts for this track. </P> <H2>References</H2> <p> Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A <em>et al</em>. -<a href="http://science.sciencemag.org/content/296/5566/261.2" target="_blank"> +<a href="https://science.sciencemag.org/content/296/5566/261.2" target="_blank"> A human genome diversity cell line panel</a>. <em>Science</em>. 2002 Apr 12;296(5566):261-2. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11954565" target="_blank">11954565</a> </p> <p> Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL <em>et al</em>. -<a href="http://science.sciencemag.org/content/319/5866/1100" target="_blank"> +<a href="https://science.sciencemag.org/content/319/5866/1100" target="_blank"> Worldwide human relationships inferred from genome-wide patterns of variation</a>. <em>Science</em>. 2008 Feb 22;319(5866):1100-4. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18292342" target="_blank">18292342</a> </p> <p> Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW <em>et al</em>. <a href="https://genome.cshlp.org/content/19/5/826.long" target="_blank"> Signals of recent positive selection in a worldwide sample of human populations</a>. <em>Genome Res</em>. 2009 May;19(5):826-37. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19307593" target="_blank">19307593</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675971/" target="_blank">PMC2675971</a> </p> <P> Wessel P, Smith WHF. <a href="https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/98EO00426" target="_blank"> New, improved version of Generic Mapping Tools released</a>. <em>EOS, Trans. Amer. Geophys. U.</em> 1998;79(47):579.</P>