converting genotype data in linux

[nomad01]

Could any linux user on the forum try to covert this dataset into plink format? (I'm on Windows)

The dataset is here under "Toward a more Uniform Sampling of Human Genetic Diversity"
https://jorde.genetics.utah.edu/published-data/

The code to do so is here:
https://www.harappadna.org/2011/04/xing-...onversion/

[AimSmall]

That was interesting.  Learned something.  Uploading... hang tight.

Link is good for three days.

https://we.tl/t-Ca6fqa2Y4m

Code:

Options in effect:
  --make-bed
  --missing-genotype N
  --out xing
  --output-missing-genotype 0
  --tfile xing

15891 MB RAM detected; reserving 7945 MB for main workspace.
Processing .tped file... done.
xing-temporary.bed + xing-temporary.bim + xing-temporary.fam written.
246554 variants loaded from .bim file.
850 people (0 males, 0 females, 850 ambiguous) loaded from .fam.
Ambiguous sex IDs written to xing.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 850 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.991105.
246554 variants and 850 people pass filters and QC.
Note: No phenotypes present.
--make-bed to xing.bed + xing.bim + xing.fam ... done.

Kind of low SNP count.  Be curious what your research finds.

You might want to change all of those -9s in the family file to prevent issues with some tools. I'd make them a 1.

[AimSmall]

It has some clustering within...  quick and dirty PLINK PCA 25 and super simple plot.

   

For clarification, those X & Y are the first two vectors of the PCA. The first two columns of the eigenvector file are labels.

[AimSmall]

No wonder... found the paper.  These samples are from all over the world.  The dataset has no population information, just sample names.  I had no idea what was within.  Just data to me at that point.

https://www.sciencedirect.com/science/ar...via%3Dihub

   

[AimSmall]

Ok.... the original data in the CSVs contains not only the population names, but also the continent. Going to see if I can add the popnames to the fam file.

The conversion script didn't attempt to keep the additional information.

[nomad01]

That was interesting.  Learned something.  Uploading... hang tight.

Link is good for three days.

https://we.tl/t-Ca6fqa2Y4m

Code:

Options in effect:
  --make-bed
  --missing-genotype N
  --out xing
  --output-missing-genotype 0
  --tfile xing

15891 MB RAM detected; reserving 7945 MB for main workspace.
Processing .tped file... done.
xing-temporary.bed + xing-temporary.bim + xing-temporary.fam written.
246554 variants loaded from .bim file.
850 people (0 males, 0 females, 850 ambiguous) loaded from .fam.
Ambiguous sex IDs written to xing.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 850 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.991105.
246554 variants and 850 people pass filters and QC.
Note: No phenotypes present.
--make-bed to xing.bed + xing.bim + xing.fam ... done.

Kind of low SNP count.  Be curious what your research finds.

You might want to change all of those -9s in the family file to prevent issues with some tools.  I'd make them a 1.

Thanks!

[nomad01]

Ok.... the original data in the CSVs contains not only the population names, but also the continent.  Going to see if I can add the popnames to the fam file.

The conversion script didn't attempt to keep the additional information.

There's a table with supplementary info on the Jorde Lab website

[AimSmall]

Ok.... the original data in the CSVs contains not only the population names, but also the continent.  Going to see if I can add the popnames to the fam file.

The conversion script didn't attempt to keep the additional information.

[AimSmall]

Well, had to modify my script.  The fam file is space delimited and the populations being imported had spaces in the name so I had to modify to replace those with underscores.

Code:

Alur AFA1 0 0 0 1
Alur AFA12 0 0 0 1
Alur AFA2 0 0 0 1
Alur AFA3 0 0 0 1
Alur AFA4 0 0 0 1
Alur AFA5 0 0 0 1
Alur AFA6 0 0 0 1
Alur AFA7 0 0 0 1
Alur AFA8 0 0 0 1
Alur AFA9 0 0 0 1
Hema AFH1 0 0 0 1
Hema AFH10 0 0 0 1
Hema AFH11 0 0 0 1
Hema AFH12 0 0 0 1
Hema AFH13 0 0 0 1
Hema AFH15 0 0 0 1
Hema AFH16 0 0 0 1
Hema AFH2 0 0 0 1
Hema AFH3 0 0 0 1
Hema AFH4 0 0 0 1
Hema AFH5 0 0 0 1
Hema AFH6 0 0 0 1
Hema AFH7 0 0 0 1
Hema AFH8 0 0 0 1
Hema AFH9 0 0 0 1
Pygmy AFP10 0 0 0 1
Pygmy AFP11 0 0 0 1
Pygmy AFP12 0 0 0 1
Pygmy AFP13 0 0 0 1
Pygmy AFP14 0 0 0 1
Pygmy AFP15 0 0 0 1
Pygmy AFP19 0 0 0 1
Pygmy AFP2 0 0 0 1
Pygmy AFP20 0 0 0 1
Pygmy AFP21 0 0 0 1
Pygmy AFP24 0 0 0 1
Pygmy AFP25 0 0 0 1
Pygmy AFP26 0 0 0 1
Pygmy AFP28 0 0 0 1
Pygmy AFP29 0 0 0 1
Pygmy AFP3 0 0 0 1
Pygmy AFP32 0 0 0 1
Pygmy AFP33 0 0 0 1
Pygmy AFP34 0 0 0 1
Pygmy AFP4 0 0 0 1
Pygmy AFP5 0 0 0 1
Pygmy AFP6 0 0 0 1
Pygmy AFP7 0 0 0 1
Pygmy AFP8 0 0 0 1
Pygmy AFP9 0 0 0 1
AP_Brahmin B11 0 0 0 1
AP_Brahmin B3 0 0 0 1
AP_Brahmin BN50 0 0 0 1
AP_Brahmin BN51 0 0 0 1
AP_Brahmin BN52 0 0 0 1
AP_Brahmin BN9 0 0 0 1
AP_Brahmin BV10 0 0 0 1
AP_Brahmin BV19 0 0 0 1
AP_Brahmin BV2 0 0 0 1
AP_Brahmin BV25 0 0 0 1
AP_Brahmin BV29 0 0 0 1
AP_Brahmin BV32 0 0 0 1
AP_Brahmin BV33 0 0 0 1
AP_Brahmin BV34 0 0 0 1
AP_Brahmin BV35 0 0 0 1
AP_Brahmin BV36 0 0 0 1
AP_Brahmin BV38 0 0 0 1
AP_Brahmin BV39 0 0 0 1
AP_Brahmin BV4 0 0 0 1
AP_Brahmin BV40 0 0 0 1
AP_Brahmin BV42 0 0 0 1
AP_Brahmin BV43 0 0 0 1
AP_Brahmin BV44 0 0 0 1
AP_Brahmin BV45 0 0 0 1
AP_Brahmin BV5 0 0 0 1
N._European C10032 0 0 0 1
N._European C10066 0 0 0 1
N._European C10078 0 0 0 1
N._European C10079 0 0 0 1
N._European C10116 0 0 0 1
N._European C10171 0 0 0 1
N._European C10307 0 0 0 1
N._European C10398 0 0 0 1
N._European C10452 0 0 0 1
N._European C10500 0 0 0 1
N._European C10524 0 0 0 1
N._European C10605 0 0 0 1
N._European C10624 0 0 0 1
N._European C10685 0 0 0 1
N._European C10709 0 0 0 1
N._European C10741 0 0 0 1
N._European C10750 0 0 0 1
N._European C10764 0 0 0 1
N._European C10774 0 0 0 1
N._European C11023 0 0 0 1
N._European C11090 0 0 0 1
N._European C11102 0 0 0 1
N._European C11106 0 0 0 1
N._European C11108 0 0 0 1
N._European C4905 0 0 0 1
Khmer_Cambodian CAM11373 0 0 0 1
Khmer_Cambodian CAM11374 0 0 0 1
Khmer_Cambodian CAM11375 0 0 0 1
Khmer_Cambodian CAM11376 0 0 0 1
Khmer_Cambodian CAM11377 0 0 0 1
Chinese CHI10 0 0 0 1
Chinese CHI11321 0 0 0 1
Chinese CHI11322 0 0 0 1
Chinese CHI11323 0 0 0 1
Chinese CHI11324 0 0 0 1
Chinese CHI11325 0 0 0 1
Chinese CHI18 0 0 0 1
Samoan F003899 0 0 0 1
Samoan F006770 0 0 0 1
Samoan F006982 0 0 0 1
Tongan F007961 0 0 0 1
Samoan F007966 0 0 0 1
Tongan F007981 0 0 0 1
Samoan F012352 0 0 0 1
Samoan F012972 0 0 0 1
Tongan F021082 0 0 0 1
Samoan F021545 0 0 0 1
Tongan F021743 0 0 0 1
Samoan F021875 0 0 0 1
Tongan F021949 0 0 0 1
Samoan F024892 0 0 0 1
Samoan F024893 0 0 0 1
Samoan F024894 0 0 0 1
Tongan F024897 0 0 0 1
Samoan F024898 0 0 0 1
Samoan F025015 0 0 0 1
Tongan F025017 0 0 0 1
Tongan F025054 0 0 0 1
Tongan F025122 0 0 0 1
Slovenian F037395 0 0 0 1
Slovenian F037870 0 0 0 1
Slovenian F037872 0 0 0 1
Slovenian F037892 0 0 0 1
Slovenian F037911 0 0 0 1
Slovenian F037921 0 0 0 1
Slovenian F037924 0 0 0 1
Slovenian F037925 0 0 0 1
Slovenian F037926 0 0 0 1
Slovenian F038033 0 0 0 1
Slovenian F038074 0 0 0 1
Slovenian F038083 0 0 0 1
Slovenian F038210 0 0 0 1
Slovenian F038211 0 0 0 1
Slovenian F038235 0 0 0 1
Slovenian F038247 0 0 0 1
Slovenian F038257 0 0 0 1
Slovenian F038306 0 0 0 1
Slovenian F038327 0 0 0 1
Slovenian F038350 0 0 0 1
Slovenian F038376 0 0 0 1
Slovenian F038390 0 0 0 1
Slovenian F038394 0 0 0 1
Slovenian F038408 0 0 0 1
Slovenian F038433 0 0 0 1
Totonac F038849 0 0 0 1
Totonac F038856 0 0 0 1
Totonac F038867 0 0 0 1
Totonac F038878 0 0 0 1
Totonac F038885 0 0 0 1
Totonac F038895 0 0 0 1
Totonac F038903 0 0 0 1
Totonac F038917 0 0 0 1
Totonac F038922 0 0 0 1
Totonac F038936 0 0 0 1
Totonac F038939 0 0 0 1
Totonac F038941 0 0 0 1
Totonac F038947 0 0 0 1
Totonac F038949_A 0 0 0 1
Totonac F038949_B 0 0 0 1
Totonac F038953 0 0 0 1
Totonac F038958 0 0 0 1
Totonac F038972 0 0 0 1
Totonac F038974 0 0 0 1
Totonac F038975 0 0 0 1
Totonac F038985 0 0 0 1
Totonac F038987 0 0 0 1
Totonac F038995 0 0 0 1
Totonac F039013 0 0 0 1
Tongan F039922 0 0 0 1
Tongan F039933 0 0 0 1
Tongan F039937 0 0 0 1
Tongan F039955 0 0 0 1
Bambaran F045400 0 0 0 1
Bambaran F045403 0 0 0 1
Bambaran F045415 0 0 0 1
Bambaran F045434 0 0 0 1
Bambaran F045438 0 0 0 1
Bambaran F045452 0 0 0 1
Bambaran F045455 0 0 0 1
Bambaran F054732 0 0 0 1
Bambaran F054756 0 0 0 1
Bambaran F054771 0 0 0 1
Bambaran F054776 0 0 0 1
Bambaran F054779 0 0 0 1
Bambaran F055505 0 0 0 1
Bambaran F055575 0 0 0 1
Bambaran F055584 0 0 0 1
Bambaran F055591 0 0 0 1
Bambaran F055894 0 0 0 1
Bambaran F055901 0 0 0 1
Bambaran F055906 0 0 0 1
Bambaran F055968 0 0 0 1
Bambaran F056709 0 0 0 1
Bambaran F056802 0 0 0 1
Bambaran F056820 0 0 0 1
Bambaran F056855 0 0 0 1
Bambaran F056858 0 0 0 1
Dogon F058364 0 0 0 1
Dogon F058366 0 0 0 1
Dogon F058369 0 0 0 1
Dogon F058373 0 0 0 1
Dogon F058379 0 0 0 1
Dogon F058383 0 0 0 1
Dogon F058387 0 0 0 1
Dogon F058391 0 0 0 1
Dogon F058399 0 0 0 1
Dogon F058413 0 0 0 1
Dogon F058421 0 0 0 1
Dogon F058426 0 0 0 1
Dogon F058431 0 0 0 1
Dogon F058436 0 0 0 1
Dogon F058446 0 0 0 1
Dogon F058451 0 0 0 1
Dogon F058454 0 0 0 1
Dogon F058465 0 0 0 1
Dogon F058472 0 0 0 1
Dogon F058494 0 0 0 1
Dogon F058498 0 0 0 1
Dogon F058500 0 0 0 1
Dogon F058510 0 0 0 1
Dogon F058517 0 0 0 1
Kyrgyzstani F063030 0 0 0 1
Kyrgyzstani F063040 0 0 0 1
Kyrgyzstani F063055 0 0 0 1
Kyrgyzstani F063068 0 0 0 1
Kyrgyzstani F063070 0 0 0 1
Kyrgyzstani F063072 0 0 0 1
Kyrgyzstani F063074 0 0 0 1
Kyrgyzstani F063080 0 0 0 1
Kyrgyzstani F063081 0 0 0 1
Kyrgyzstani F063088 0 0 0 1
Kyrgyzstani F063098 0 0 0 1
Kyrgyzstani F063296 0 0 0 1
Kyrgyzstani F063303 0 0 0 1
Kyrgyzstani F063319 0 0 0 1
Kyrgyzstani F063323 0 0 0 1
Kyrgyzstani F063345 0 0 0 1
Kyrgyzstani F063348 0 0 0 1
Kyrgyzstani F063359 0 0 0 1
Kyrgyzstani F063360 0 0 0 1
Kyrgyzstani F063368 0 0 0 1
Kyrgyzstani F063397 0 0 0 1
Kyrgyzstani F063402 0 0 0 1
Kyrgyzstani F063423 0 0 0 1
Kyrgyzstani F063447 0 0 0 1
Kyrgyzstani F063448 0 0 0 1
Kurd F063722 0 0 0 1
Kurd F063728 0 0 0 1
Kurd F063752 0 0 0 1
Kurd F063761 0 0 0 1
Kurd F063763 0 0 0 1
Kurd F063771 0 0 0 1
Kurd F063787 0 0 0 1
Kurd F063791 0 0 0 1
Kurd F063795 0 0 0 1
Kurd F063796 0 0 0 1
Kurd F063803 0 0 0 1
Kurd F063805 0 0 0 1
Kurd F063808 0 0 0 1
Kurd F063821 0 0 0 1
Kurd F063824 0 0 0 1
Kurd F063832 0 0 0 1
Kurd F063834 0 0 0 1
Kurd F063838 0 0 0 1
Kurd F063856 0 0 0 1
Kurd F063863 0 0 0 1
Kurd F063867 0 0 0 1
Kurd F063873 0 0 0 1
Kurd F063886 0 0 0 1
Kurd F063888 0 0 0 1
Bolivian F065038 0 0 0 1
Bolivian F065040 0 0 0 1
Bolivian F065042 0 0 0 1
Bolivian F065054 0 0 0 1
Bolivian F065081 0 0 0 1
Bolivian F065091 0 0 0 1
Bolivian F065101 0 0 0 1
Bolivian F065105 0 0 0 1
Thai F066566 0 0 0 1
Thai F066571 0 0 0 1
Thai F066579 0 0 0 1
Thai F066580 0 0 0 1
Thai F066582 0 0 0 1
Thai F066585 0 0 0 1
Thai F066586 0 0 0 1
Thai F066599 0 0 0 1
Thai F066600 0 0 0 1
Thai F066607 0 0 0 1
Thai F066608 0 0 0 1
Thai F066609 0 0 0 1
Thai F066611 0 0 0 1
Thai F066612 0 0 0 1
Thai F066613 0 0 0 1
Pakistani F067238 0 0 0 1
Pakistani F067264 0 0 0 1
Bolivian F067928 0 0 0 1
Bolivian F067947 0 0 0 1
Bolivian F068172 0 0 0 1
Bolivian F068184 0 0 0 1
Bolivian F068237 0 0 0 1
Pakistani F069185 0 0 0 1
Pakistani F069209 0 0 0 1
Pakistani F069316 0 0 0 1
Buryat F071508 0 0 0 1
Buryat F071512 0 0 0 1
Buryat F071533 0 0 0 1
Buryat F071535 0 0 0 1
Buryat F071588 0 0 0 1
Buryat F071597 0 0 0 1
Buryat F071735 0 0 0 1
Buryat F071799 0 0 0 1
Buryat F071805 0 0 0 1
Buryat F071812 0 0 0 1
Buryat F071816 0 0 0 1
Buryat F071817 0 0 0 1
Buryat F071820 0 0 0 1
Buryat F071823 0 0 0 1
Buryat F071824 0 0 0 1
Buryat F071827 0 0 0 1
Buryat F071838 0 0 0 1
Buryat F071915 0 0 0 1
Buryat F071949 0 0 0 1
Buryat F071963 0 0 0 1
Buryat F071976 0 0 0 1
Buryat F072084 0 0 0 1
Buryat F072153 0 0 0 1
Buryat F072171 0 0 0 1
Bolivian F073415 0 0 0 1
Bolivian F073421 0 0 0 1
Bolivian F073445 0 0 0 1
Bolivian F073455 0 0 0 1
Bolivian F073458 0 0 0 1
Pakistani F073465 0 0 0 1
Pakistani F073479 0 0 0 1
Pakistani F073480 0 0 0 1
Pakistani F073495 0 0 0 1
Pakistani F073500 0 0 0 1
Pakistani F073540 0 0 0 1
Pakistani F073556 0 0 0 1
Pakistani F074899 0 0 0 1
Pakistani F074903 0 0 0 1
Pakistani F074908 0 0 0 1
Pakistani F075067 0 0 0 1
Pakistani F075092 0 0 0 1
Pakistani F076291 0 0 0 1
Pakistani F076303 0 0 0 1
Pakistani F076328 0 0 0 1
Pakistani F078117 0 0 0 1
Nepalese F078337 0 0 0 1
Nepalese F078351 0 0 0 1
Nepalese F078379 0 0 0 1
Nepalese F078399 0 0 0 1
Nepalese F078402 0 0 0 1
Nepalese F078412 0 0 0 1
Buryat F078706 0 0 0 1
Bolivian F080792 0 0 0 1
Bolivian F080817 0 0 0 1
Bolivian F080853 0 0 0 1
Bolivian F080860 0 0 0 1
Bolivian F080869 0 0 0 1
Nepalese F081366 0 0 0 1
Nepalese F081373 0 0 0 1
Nepalese F081376 0 0 0 1
Nepalese F081414 0 0 0 1
Nepalese F081419 0 0 0 1
Nepalese F081430 0 0 0 1
Nepalese F081438 0 0 0 1
Nepalese F081448 0 0 0 1
Nepalese F081455 0 0 0 1
Nepalese F081459 0 0 0 1
Nepalese F081461 0 0 0 1
Pakistani F082466 0 0 0 1
Pakistani F082470 0 0 0 1
Pakistani F082478 0 0 0 1
Pakistani F082481 0 0 0 1
Slovenian F088093 0 0 0 1
Thai F088094 0 0 0 1
Thai F088126 0 0 0 1
Thai F089307 0 0 0 1
Thai F089318 0 0 0 1
Thai F089359 0 0 0 1
Thai F089379 0 0 0 1
Thai F089398 0 0 0 1
Thai F089408 0 0 0 1
Thai F089863 0 0 0 1
Nepalese F090707 0 0 0 1
Nepalese F090727 0 0 0 1
Nepalese F090751 0 0 0 1
Nepalese F090754 0 0 0 1
Nepalese F091074 0 0 0 1
Nepalese F092519 0 0 0 1
TN_Dalit HAR1 0 0 0 1
TN_Dalit HAR10 0 0 0 1
TN_Dalit HAR11 0 0 0 1
TN_Dalit HAR12 0 0 0 1
TN_Dalit HAR14 0 0 0 1
TN_Dalit HAR2 0 0 0 1
TN_Dalit HAR3 0 0 0 1
TN_Dalit HAR4 0 0 0 1
TN_Dalit HAR5 0 0 0 1
TN_Dalit HAR6 0 0 0 1
TN_Dalit HAR7 0 0 0 1
TN_Dalit HAR8 0 0 0 1
TN_Dalit HAR9 0 0 0 1
Irula I1 0 0 0 1
Irula I10 0 0 0 1
Irula I11 0 0 0 1
Irula I12 0 0 0 1
Irula I13 0 0 0 1
Irula I14 0 0 0 1
Irula I15 0 0 0 1
Irula I16 0 0 0 1
Irula I17 0 0 0 1
Irula I19 0 0 0 1
Irula I2 0 0 0 1
Irula I20 0 0 0 1
Irula I23 0 0 0 1
Irula I25 0 0 0 1
Irula I26 0 0 0 1
Irula I27 0 0 0 1
Irula I28 0 0 0 1
Irula I3 0 0 0 1
Irula I4 0 0 0 1
Irula I5 0 0 0 1
Irula I6 0 0 0 1
Irula I7 0 0 0 1
Irula I8 0 0 0 1
Irula I9 0 0 0 1
Japanese JAP11589 0 0 0 1
Japanese JAP11590 0 0 0 1
Japanese JAP1424 0 0 0 1
Japanese JAP1425 0 0 0 1
Japanese JAP1788 0 0 0 1
Japanese JAP24 0 0 0 1
Japanese JAP26 0 0 0 1
Japanese JAP3 0 0 0 1
Japanese JAP35 0 0 0 1
Japanese JAP39 0 0 0 1
Japanese JAP48 0 0 0 1
Japanese JAP50 0 0 0 1
Japanese JAP9 0 0 0 1
AP_Madiga M11 0 0 0 1
AP_Madiga M12 0 0 0 1
AP_Madiga M13 0 0 0 1
AP_Madiga M15 0 0 0 1
AP_Madiga M16 0 0 0 1
AP_Madiga M17 0 0 0 1
AP_Madiga M18 0 0 0 1
AP_Madiga M3 0 0 0 1
AP_Madiga M4 0 0 0 1
AP_Madiga M7 0 0 0 1
AP_Mala ML1 0 0 0 1
AP_Mala ML10 0 0 0 1
AP_Mala ML12 0 0 0 1
AP_Mala ML13 0 0 0 1
AP_Mala ML14 0 0 0 1
AP_Mala ML16 0 0 0 1
AP_Mala ML5 0 0 0 1
AP_Mala ML6 0 0 0 1
AP_Mala ML7 0 0 0 1
AP_Mala ML8 0 0 0 1
AP_Mala ML9 0 0 0 1
CEU NA06985 0 0 0 1
CEU NA06993 0 0 0 1
CEU NA06994 0 0 0 1
CEU NA07000 0 0 0 1
CEU NA07022 0 0 0 1
CEU NA07034 0 0 0 1
CEU NA07055 0 0 0 1
CEU NA07056 0 0 0 1
CEU NA07345 0 0 0 1
CEU NA07357 0 0 0 1
CEU NA11829 0 0 0 1
CEU NA11830 0 0 0 1
CEU NA11831 0 0 0 1
CEU NA11832 0 0 0 1
CEU NA11839 0 0 0 1
CEU NA11840 0 0 0 1
CEU NA11881 0 0 0 1
CEU NA11882 0 0 0 1
CEU NA11992 0 0 0 1
CEU NA11993 0 0 0 1
CEU NA11994 0 0 0 1
CEU NA11995 0 0 0 1
CEU NA12003 0 0 0 1
CEU NA12004 0 0 0 1
CEU NA12005 0 0 0 1
CEU NA12006 0 0 0 1
CEU NA12043 0 0 0 1
CEU NA12044 0 0 0 1
CEU NA12056 0 0 0 1
CEU NA12057 0 0 0 1
CEU NA12144 0 0 0 1
CEU NA12145 0 0 0 1
CEU NA12146 0 0 0 1
CEU NA12154 0 0 0 1
CEU NA12155 0 0 0 1
CEU NA12156 0 0 0 1
CEU NA12234 0 0 0 1
CEU NA12236 0 0 0 1
CEU NA12239 0 0 0 1
CEU NA12248 0 0 0 1
CEU NA12249 0 0 0 1
CEU NA12264 0 0 0 1
CEU NA12716 0 0 0 1
CEU NA12717 0 0 0 1
CEU NA12750 0 0 0 1
CEU NA12751 0 0 0 1
CEU NA12760 0 0 0 1
CEU NA12761 0 0 0 1
CEU NA12762 0 0 0 1
CEU NA12763 0 0 0 1
CEU NA12812 0 0 0 1
CEU NA12813 0 0 0 1
CEU NA12814 0 0 0 1
CEU NA12815 0 0 0 1
CEU NA12872 0 0 0 1
CEU NA12873 0 0 0 1
CEU NA12874 0 0 0 1
CEU NA12875 0 0 0 1
CEU NA12891 0 0 0 1
CEU NA12892 0 0 0 1
YRI NA18501 0 0 0 1
YRI NA18502 0 0 0 1
YRI NA18504 0 0 0 1
YRI NA18505 0 0 0 1
YRI NA18507 0 0 0 1
YRI NA18508 0 0 0 1
YRI NA18516 0 0 0 1
YRI NA18517 0 0 0 1
YRI NA18522 0 0 0 1
YRI NA18523 0 0 0 1
CHB NA18524 0 0 0 1
CHB NA18526 0 0 0 1
CHB NA18529 0 0 0 1
CHB NA18532 0 0 0 1
CHB NA18537 0 0 0 1
CHB NA18540 0 0 0 1
CHB NA18542 0 0 0 1
CHB NA18545 0 0 0 1
CHB NA18547 0 0 0 1
CHB NA18550 0 0 0 1
CHB NA18552 0 0 0 1
CHB NA18555 0 0 0 1
CHB NA18558 0 0 0 1
CHB NA18561 0 0 0 1
CHB NA18562 0 0 0 1
CHB NA18563 0 0 0 1
CHB NA18564 0 0 0 1
CHB NA18566 0 0 0 1
CHB NA18570 0 0 0 1
CHB NA18571 0 0 0 1
CHB NA18572 0 0 0 1
CHB NA18573 0 0 0 1
CHB NA18576 0 0 0 1
CHB NA18577 0 0 0 1
CHB NA18579 0 0 0 1
CHB NA18582 0 0 0 1
CHB NA18592 0 0 0 1
CHB NA18593 0 0 0 1
CHB NA18594 0 0 0 1
CHB NA18603 0 0 0 1
CHB NA18605 0 0 0 1
CHB NA18608 0 0 0 1
CHB NA18609 0 0 0 1
CHB NA18611 0 0 0 1
CHB NA18612 0 0 0 1
CHB NA18620 0 0 0 1
CHB NA18621 0 0 0 1
CHB NA18622 0 0 0 1
CHB NA18623 0 0 0 1
CHB NA18624 0 0 0 1
CHB NA18632 0 0 0 1
CHB NA18633 0 0 0 1
CHB NA18635 0 0 0 1
CHB NA18636 0 0 0 1
CHB NA18637 0 0 0 1
YRI NA18852 0 0 0 1
YRI NA18853 0 0 0 1
YRI NA18855 0 0 0 1
YRI NA18856 0 0 0 1
YRI NA18858 0 0 0 1
YRI NA18859 0 0 0 1
YRI NA18861 0 0 0 1
YRI NA18862 0 0 0 1
YRI NA18870 0 0 0 1
YRI NA18871 0 0 0 1
YRI NA18912 0 0 0 1
YRI NA18913 0 0 0 1
JPT NA18940 0 0 0 1
JPT NA18942 0 0 0 1
JPT NA18943 0 0 0 1
JPT NA18944 0 0 0 1
JPT NA18945 0 0 0 1
JPT NA18947 0 0 0 1
JPT NA18948 0 0 0 1
JPT NA18949 0 0 0 1
JPT NA18951 0 0 0 1
JPT NA18952 0 0 0 1
JPT NA18953 0 0 0 1
JPT NA18956 0 0 0 1
JPT NA18959 0 0 0 1
JPT NA18960 0 0 0 1
JPT NA18961 0 0 0 1
JPT NA18964 0 0 0 1
JPT NA18965 0 0 0 1
JPT NA18966 0 0 0 1
JPT NA18967 0 0 0 1
JPT NA18968 0 0 0 1
JPT NA18969 0 0 0 1
JPT NA18970 0 0 0 1
JPT NA18971 0 0 0 1
JPT NA18972 0 0 0 1
JPT NA18973 0 0 0 1
JPT NA18974 0 0 0 1
JPT NA18975 0 0 0 1
JPT NA18976 0 0 0 1
JPT NA18978 0 0 0 1
JPT NA18980 0 0 0 1
JPT NA18981 0 0 0 1
JPT NA18987 0 0 0 1
JPT NA18990 0 0 0 1
JPT NA18991 0 0 0 1
JPT NA18992 0 0 0 1
JPT NA18994 0 0 0 1
JPT NA18995 0 0 0 1
JPT NA18997 0 0 0 1
JPT NA18998 0 0 0 1
JPT NA18999 0 0 0 1
JPT NA19000 0 0 0 1
JPT NA19003 0 0 0 1
JPT NA19005 0 0 0 1
JPT NA19007 0 0 0 1
JPT NA19012 0 0 0 1
Luhya NA19020 0 0 0 1
Luhya NA19027 0 0 0 1
Luhya NA19028 0 0 0 1
Luhya NA19031 0 0 0 1
Luhya NA19035 0 0 0 1
Luhya NA19041 0 0 0 1
Luhya NA19044 0 0 0 1
Luhya NA19046 0 0 0 1
YRI NA19092 0 0 0 1
YRI NA19093 0 0 0 1
YRI NA19098 0 0 0 1
YRI NA19099 0 0 0 1
YRI NA19101 0 0 0 1
YRI NA19102 0 0 0 1
YRI NA19116 0 0 0 1
YRI NA19119 0 0 0 1
YRI NA19127 0 0 0 1
YRI NA19128 0 0 0 1
YRI NA19130 0 0 0 1
YRI NA19131 0 0 0 1
YRI NA19137 0 0 0 1
YRI NA19138 0 0 0 1
YRI NA19140 0 0 0 1
YRI NA19141 0 0 0 1
YRI NA19143 0 0 0 1
YRI NA19144 0 0 0 1
YRI NA19152 0 0 0 1
YRI NA19153 0 0 0 1
YRI NA19159 0 0 0 1
YRI NA19160 0 0 0 1
YRI NA19171 0 0 0 1
YRI NA19172 0 0 0 1
YRI NA19192 0 0 0 1
YRI NA19193 0 0 0 1
YRI NA19200 0 0 0 1
YRI NA19201 0 0 0 1
YRI NA19203 0 0 0 1
YRI NA19204 0 0 0 1
YRI NA19206 0 0 0 1
YRI NA19207 0 0 0 1
YRI NA19209 0 0 0 1
YRI NA19210 0 0 0 1
YRI NA19222 0 0 0 1
YRI NA19223 0 0 0 1
YRI NA19238 0 0 0 1
YRI NA19239 0 0 0 1
Luhya NA19307 0 0 0 1
Luhya NA19308 0 0 0 1
Luhya NA19309 0 0 0 1
Luhya NA19311 0 0 0 1
Luhya NA19312 0 0 0 1
Luhya NA19317 0 0 0 1
Luhya NA19318 0 0 0 1
Luhya NA19319 0 0 0 1
Luhya NA19331 0 0 0 1
Luhya NA19334 0 0 0 1
Luhya NA19346 0 0 0 1
Luhya NA19350 0 0 0 1
Luhya NA19352 0 0 0 1
Luhya NA19359 0 0 0 1
Luhya NA19360 0 0 0 1
Luhya NA19371 0 0 0 1
Tuscan NA20509 0 0 0 1
Tuscan NA20510 0 0 0 1
Tuscan NA20512 0 0 0 1
Tuscan NA20515 0 0 0 1
Tuscan NA20516 0 0 0 1
Tuscan NA20518 0 0 0 1
Tuscan NA20519 0 0 0 1
Tuscan NA20520 0 0 0 1
Tuscan NA20521 0 0 0 1
Tuscan NA20524 0 0 0 1
Tuscan NA20525 0 0 0 1
Tuscan NA20527 0 0 0 1
Tuscan NA20528 0 0 0 1
Tuscan NA20534 0 0 0 1
Tuscan NA20538 0 0 0 1
Tuscan NA20539 0 0 0 1
Tuscan NA20543 0 0 0 1
Tuscan NA20544 0 0 0 1
Tuscan NA20581 0 0 0 1
Tuscan NA20586 0 0 0 1
Tuscan NA20588 0 0 0 1
Tuscan NA20752 0 0 0 1
Tuscan NA20754 0 0 0 1
Tuscan NA20755 0 0 0 1
Tuscan NA20758 0 0 0 1
!Kung OM111 0 0 0 1
!Kung OM117 0 0 0 1
!Kung OM128 0 0 0 1
!Kung OM133 0 0 0 1
!Kung OM134 0 0 0 1
!Kung OM137 0 0 0 1
!Kung OM140 0 0 0 1
!Kung OM141 0 0 0 1
!Kung OM144 0 0 0 1
!Kung OM148 0 0 0 1
!Kung OM54 0 0 0 1
!Kung OM63 0 0 0 1
!Kung OM98 0 0 0 1
Pedi PED17 0 0 0 1
Pedi PED20 0 0 0 1
Pedi PED32 0 0 0 1
Pedi PED38 0 0 0 1
Pedi PED54 0 0 0 1
Pedi PED55 0 0 0 1
Pedi PED57 0 0 0 1
Pedi PED58 0 0 0 1
Pedi PED59 0 0 0 1
Pedi PED60 0 0 0 1
Sotho/Tswana SOT44 0 0 0 1
Sotho/Tswana SOT48 0 0 0 1
Sotho/Tswana SOT62 0 0 0 1
Nepalese SS231506 0 0 0 1
Nepalese SS231535 0 0 0 1
Stalskoe STAL12 0 0 0 1
Stalskoe STAL19 0 0 0 1
Stalskoe STAL24 0 0 0 1
Stalskoe STAL25 0 0 0 1
Stalskoe STAL35 0 0 0 1
Iban SW009 0 0 0 1
Iban SW010 0 0 0 1
Iban SW016 0 0 0 1
Iban SW019 0 0 0 1
Iban SW024 0 0 0 1
Iban SW027 0 0 0 1
Iban SW029 0 0 0 1
Iban SW033 0 0 0 1
Iban SW034 0 0 0 1
Iban SW040 0 0 0 1
Iban SW043 0 0 0 1
Iban SW046 0 0 0 1
Iban SW067 0 0 0 1
Iban SW085 0 0 0 1
Iban SW091 0 0 0 1
Iban SW092 0 0 0 1
Iban SW095 0 0 0 1
Iban SW097 0 0 0 1
Iban SW098 0 0 0 1
Iban SW105 0 0 0 1
Iban SW107 0 0 0 1
Iban SW109 0 0 0 1
Iban SW143 0 0 0 1
Iban SW145 0 0 0 1
Iban SW152 0 0 0 1
Chinese TAW17 0 0 0 1
Chinese TAW37 0 0 0 1
Chinese TAW45 0 0 0 1
TN_Brahmin TBR1 0 0 0 1
TN_Brahmin TBR10 0 0 0 1
TN_Brahmin TBR11 0 0 0 1
TN_Brahmin TBR12 0 0 0 1
TN_Brahmin TBR13 0 0 0 1
TN_Brahmin TBR14 0 0 0 1
TN_Brahmin TBR15 0 0 0 1
TN_Brahmin TBR2 0 0 0 1
TN_Brahmin TBR3 0 0 0 1
TN_Brahmin TBR4 0 0 0 1
TN_Brahmin TBR5 0 0 0 1
TN_Brahmin TBR6 0 0 0 1
TN_Brahmin TBR7 0 0 0 1
TN_Brahmin TBR8 0 0 0 1
Sotho/Tswana TSW23 0 0 0 1
Sotho/Tswana TSW24 0 0 0 1
Sotho/Tswana TSW25 0 0 0 1
Sotho/Tswana TSW26 0 0 0 1
Sotho/Tswana TSW4 0 0 0 1
Urkarah URK1 0 0 0 1
Urkarah URK12 0 0 0 1
Urkarah URK13 0 0 0 1
Urkarah URK14 0 0 0 1
Urkarah URK18 0 0 0 1
Urkarah URK24 0 0 0 1
Urkarah URK26 0 0 0 1
Urkarah URK27 0 0 0 1
Urkarah URK29 0 0 0 1
Urkarah URK30 0 0 0 1
Urkarah URK31 0 0 0 1
Urkarah URK34 0 0 0 1
Urkarah URK36 0 0 0 1
Urkarah URK38 0 0 0 1
Urkarah URK41 0 0 0 1
Urkarah URK6 0 0 0 1
Urkarah URK7 0 0 0 1
Urkarah URK9 0 0 0 1
Vietnamese VIET16 0 0 0 1
Vietnamese VIET19 0 0 0 1
Vietnamese VIET2 0 0 0 1
Vietnamese VIET20 0 0 0 1
Vietnamese VIET23 0 0 0 1
Vietnamese VIET4 0 0 0 1
Vietnamese VIET41 0 0 0 1
Nguni ZU30 0 0 0 1
Nguni ZU33 0 0 0 1
Nguni ZU34 0 0 0 1
Nguni ZU35 0 0 0 1
Nguni ZU36 0 0 0 1
Nguni ZU38 0 0 0 1
Nguni ZU39 0 0 0 1
Nguni ZU41 0 0 0 1
Nguni ZU42 0 0 0 1

[AimSmall]

Ok.... the original data in the CSVs contains not only the population names, but also the continent.  Going to see if I can add the popnames to the fam file.

The conversion script didn't attempt to keep the additional information.

There's a table with supplementary info on the Jorde Lab website

See my modified fam file

[AimSmall]

Was reading this thread where they discussed the Xing dataset and how the Indian government was pulling samples from being shared.

https://www.harappadna.org/2011/06/chang.../#comments

This Xing dataset has Indian populations I don't find within the v62_1240K dataset and just a few in the HO.

AP_Brahmin
TN_Brahmin
TN_Dalit

[AimSmall]