{"id":38655,"date":"2011-03-14T14:55:40","date_gmt":"2011-03-14T22:55:40","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=10311"},"modified":"2011-03-14T14:55:40","modified_gmt":"2011-03-14T22:55:40","slug":"analyzing-ancestry-with-admixture-step-by-step","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2011\/03\/14\/analyzing-ancestry-with-admixture-step-by-step\/","title":{"rendered":"Analyzing ancestry with ADMIXTURE, step by step"},"content":{"rendered":"

Over the past few months I was hoping more people would start doing what Zack Ajmal<\/a>, Dienekes<\/a>, and David<\/a>, have been doing. There are public data sets, and open source software, so that anyone with nerdy inclination can explore their own questions out of curiosity. That way you can see the power and<\/em> the limitations of \u00a0genomics on your own desktop<\/strong>. I wonder if one of the biggest reasons that more people haven’t started doing this is formatting. It can be a pain to convert matrix formatted files into pedigree format, for example. But the data gusher isn’t ending, look at what’s coming out (and has come out) in the 1000 Genomes<\/a> project!<\/p>\n

I’ve been thinking I need to write up a post which is a “soft landing” for people so that we can reduce the “activation energy” for this sort of thing…once you get hooked, you only go deeper. Luckily an anonymous tipster has sent me the link to a URL with a huge data set which has been merged, already pedigree formatted. Here are the populations:<\/p>\n<\/p>\n

!Kung
\nBuryats
\nHausa
\nMada
\nPunjabi Arain
\nTotonac<\/p>\n

Adygei
\nCambodian
\nHazara
\nMakrani
\nPygmy
\nTu<\/p>\n

African Americans
\nChinese
\nHema
\nMalayan
\nRomanians
\nTujia<\/p>\n

Algeria
\nChinese Americans
\nHezhen
\nMandenka
\nRussian
\nTunisia<\/p>\n

Altaians
\nChukchis
\nHungarians
\nMaya
\nSahara Occ
\nTurks<\/p>\n

Alur
\nChuvashs
\nIban
\nMbuti
\nSakilli
\nTuscans<\/p>\n

Ap Brahmin
\nCochin Jews
\nIgbo
\nMelanesian
\nSamaritians
\nTuvinians<\/p>\n

Ap Madiga
\nColombian
\nIranian Jews
\nMexicans
\nSamoan
\nUrkarah<\/p>\n

Ap Mala
\nCypriots
\nIranians
\nMiao
\nSan
\nUtahn Whites<\/p>\n

Armenians
\nDai
\nIraq Jews
\nMongola
\nSan Nb
\nUygur<\/p>\n

Armenians B
\nDaur
\nIrula
\nMongolians
\nSandawe
\nUzbekistan Jews<\/p>\n

Ashkenazy Jews
\nDogon
\nItalian
\nMoroccans
\nSardinian
\nUzbeks<\/p>\n

Azerbaijan Jews
\nDolgans
\nJapanese
\nMorocco Jews
\nSaudis
\nVietnamese<\/p>\n

Balochi
\nDruze
\nJordanians
\nMorocco N
\nSelkups
\nGreenlanders<\/p>\n

Bambaran
\nGreenlanders
\nKaba
\nMorocco …<\/p>\n","protected":false},"excerpt":{"rendered":"

Over the past few months I was hoping more people would start doing what Zack Ajmal, Dienekes, and David, have been doing. There are public data sets, and open source software, so that anyone with nerdy inclination can explore their own questions out o…<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[290,1188,1189,1190,780,4,82,998,1191,1192,360,1193,1194],"tags":[],"class_list":["post-38655","post","type-post","status-publish","format-standard","hentry","category-admixture","category-ancestry-inference","category-bga-500k","category-c-ran","category-dodecad","category-genetics","category-genomics","category-harappa-ancestry-project","category-how-to-analyze-ancestry","category-how-to-run-admixture","category-personal-genomics","category-plink","category-r"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/38655","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/comments?post=38655"}],"version-history":[{"count":9,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/38655\/revisions"}],"predecessor-version":[{"id":38657,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/38655\/revisions\/38657"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=38655"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=38655"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=38655"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}