Dodecad k12b West & Central Asian results Vol 4.

[Kaspias]

Edit: I just remembered Plink does screw up allele order so max-maf may be affected. I normally import alleles into bim using my Hg19 reference genome using a script that i made

This explains then

[Komintasavalta]

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 . 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)

[Leto]

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.

[Lucas]

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.

[Leto]

Ok I will delete my post now, as Komintasavalta must read it as gave me thumb.

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.

[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 . 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)

I'll answer this in a new thread called "Plink questions" https://www.theapricity.com/forum/sh...ated-questions

where you can post anything Plink related such as IBS or FST

[Dr_Maul]

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

[Altaylı]

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

[RatCat]

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

[Kyp]

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 Erzurum