This explains thenQuote:
Originally Posted by Zoro
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This explains thenQuote:
Originally Posted by Zoro
How can I convert the Reich dataset to bed+bim+fam? Or is there a preconverted version of it? Or what other dataset should I use with plink? I was able to create a .bed file like this:
$ echo 'genotypename: g/v44.3_1240K_public/v44.3_1240K_public.geno
snpname: g/v44.3_1240K_public/v44.3_1240K_public.snp
indivname: g/v44.3_1240K_public/v44.3_1240K_public.ind
outputformat: PACKEDPED
genotypeoutname: example.bed
snpoutname: example.snp
indivoutname: example.ind'>parfile
$ convertf -p parfile
But how do I get the .bim and .fam?
I looked up the format of the parfile here: https://github.com/DReichLab/AdmixTo...aster/convertf. I couldn't get convertf to compile, but there was an old Mac binary here: https://github.com/chrchang/eigensoft.
Edit: The answer was to just change the filename extension of the snpoutname and indivoutname lines :picard2:. Sorry for OT.
f=g/v44.3_1240K_public/v44.3_1240K_public;o=${f##*/};convertf -p <(printf %s\\n genotypename:\ $f.geno snpname:\ $f.snp indivname:\ $f.ind outputformat:\ PACKEDPED genotypeoutname:\ $o.bed snpoutname:\ $o.bim indivoutname:\ $o.fam)
Can you please stop with this gibberish? Zoro, the Komi larper, all of you. It's fucking spam by this thread's standards! Kyp is a poor custodian of Dodecad K12b but I'm a true believer.
Ok I will delete my post now, as Komintasavalta must read it as gave me thumb.Quote:
Originally Posted by Leto
One post of yours is okay, it's mainly Zoro and unfortunately Kaspias who started this. By the way, check that thread, there's some minor renaming request.Quote:
Originally Posted by Lucas
I'll answer this in a new thread called "Plink questions" https://www.theapricity.com/forum/sh...ated-questionsQuote:
Originally Posted by Komintasavalta
where you can post anything Plink related such as IBS or FST
:focus:
Armenian. Relatively homogenous besides NA which may or may not be an error
Gedrosia 17.55 Pct
Siberian -
Northwest_African 2.54 Pct
Southeast_Asian -
Atlantic_Med 12.65 Pct
North_European 4.53 Pct
South_Asian -
East_African -
Southwest_Asian 14.65 Pct
East_Asian -
Caucasus 48.08 Pct
Sub_Saharan -
Target: Minasian
Distance: 1.2448% / 1.24479458 | ADC: 0.25x RC
59.4 Armenian_West
25.3 Armenian_East
11.0 Udi
3.4 Algerian
0.9 Sardinian
Target: Minasian
Distance: 1.2841% / 1.28406085 | R3P
90.7 Armenian_West
5.9 Kubachi_Dagestan
3.4 Algerian
Uzbek from khwarazm/Hive
Gedrosia 14 91 Pct
Siberian 12.46 Pct
Northwest_African 0.33 Pct
Southeast_Asian -
Atlantic_Med 9.86 Pct
North_European 17 Pct
South_Asian 5.61 Pct
East_African 0.22 Pct
Southwest_Asian 5.56 Pct
East_Asian 18.19 Pct
Caucasus 15.86 Pct
Sub_Saharan -
Target: Uzbek
Distance: 2.0487% / 2.04870677 | ADC: 0.25x RC
70.7 Uzbeki
11.0 Crimean_Tatar_Steppe
8.7 Spanish_Basque
4.9 Kuwait2
3.0 Nepali_Newar_Shrestha
1.7 Balkan_Gypsy
Distance to: Uzbek
8.39176978 Turkmen_Afghanistan
8.67761488 Uzbeki
9.48835075 Turkmen_Uzbekistan
11.68350547 Crimean_Tatar_Steppe
15.02058255 Nogai_Stavropol
15.84594901 Turkmen_Iran
16.72250878 Karakalpak
16.88122034 Uyghur
18.56209309 Lipka_Tatar
18.71440889 Nogai_Astrakhan
18.84798132 Hazara
18.92308114 Tajik_Mountain
20.54656419 Turkmen_TM
20.70007729 Bashkir_South
21.37961880 Tatar_Siberia
21.51706532 Tajik_Lowland
23.14635608 Nogai
23.83524072 Kazakh
24.01523683 Turk_Northwest
24.80595291 Bashkir_Central
25.22824806 Tajik_Herat
25.39767706 Turk_Southwest
25.59910741 Kyrgyz_Pamir
25.82324147 Tubalar
25.85011412 Yagnobi
I dont know the exact ethnicity she has Trabzon and Kurdish matches
Population
Gedrosia 19.38 Pct
Siberian 0.83 Pct
Northwest_African 1.78 Pct
Southeast_Asian 0.58 Pct
Atlantic_Med 9.15 Pct
North_European 7.07 Pct
South_Asian -
East_African -
Southwest_Asian 10.56 Pct
East_Asian -
Caucasus 50.64 Pct
Sub_Saharan -
Distance to: zey
3.64210104 Turk_Ahiska
4.63277455 Armenian_East
5.82734073 Udi
5.97364211 Turk_East
6.52523563 Turk_East_Black_Sea
7.12155180 Hemshin
7.67542833 Laz
7.84921652 Armenian_West
8.04954657 Greek_Pontus
8.95989397 Georgian
9.09461379 Georgian_Adjara
10.50093329 Azeri_Jew
10.54458155 Assyrian_North
10.55650510 Zaza
10.66811136 Georgian_Imereti
10.72851807 Abkhazian
10.85923570 Assyrian_West
11.07324252 Assyrian_South
11.28805563 Georgian_Gurian
11.65186251 Azerbaijani_Turkey
11.67823189 Talysh_Azerbaijan
12.66310388 Kurd_Kurmanji
12.71001967 Kurd_Adygea
12.88185157 Turk_Central_East
12.91493709 Azerbaijani_Iran
Target: zey
Distance: 1.2376% / 1.23763495 | ADC: 0.25x RC
71.3 Turk_Ahiska
14.2 Udi
11.7 Armenian_West
2.8 Algerian
Target: zey
Distance: 1.9179% / 1.91788782 | R2P
57.5 Udi
42.5 Laz
Target: zey
Distance: 1.4174% / 1.41738712 | R3P
82.0 Turk_Ahiska
10.9 Kurd_Adygea
7.1 Morocco_Jews
Target: zey
Distance: 0.9789% / 0.97890193 | R4P
62.3 Laz
21.9 Kurd_Adygea
12.5 Ingush
3.3 Algerian
Looks like from somwhere around ErzurumQuote:
Originally Posted by RatCat