qpAdm thread

**Kaspias** · 02-27-2021, 05:32 PM

Originally Posted by vbnetkhio

try with this one...
https://filebin.net/c73ep7a8u1pfgtxw

the "space" version should work with the older version of plink, the other one with the newer.

This did not work either. But I was able to convert my data to plink. I could not do it by using python at first stage but then when used conda it worked.

Edit: I fixed the other problem too. But still stuck while extracting populations...

**Kaspias** · 03-02-2021, 05:01 PM

First run:

√ 1379990 SNPs read in total
! 6558 SNPs remain after filtering. 6468 are polymorphic.

Code:

 target      left      weight     se     z
                  
1 Kaspias Turkmen    0.164 0.0991  1.65
2 Kaspias Bulgarian  0.836 0.0991  8.44

Many thanks to @Korialstrasz for the tutorial also to @vbnetkhio and @Zoro for giving a hand. I'd like to see some feedback on it, so I can try to improve.

**Zoro** · 03-02-2021, 05:33 PM

Originally Posted by Kaspias

First run:

√ 1379990 SNPs read in total
! 6558 SNPs remain after filtering. 6468 are polymorphic.

Code:

 target      left      weight     se     z
                  
1 Kaspias Turkmen    0.164 0.0991  1.65
2 Kaspias Bulgarian  0.836 0.0991  8.44

Many thanks to @Korialstrasz for the tutorial also to @vbnetkhio and @Zoro for giving a hand. I'd like to see some feedback on it, so I can try to improve.

6558 SNPs is too low to do an accurate comparison. Even though you weren't WGS genotyped I can still get you up to about 74,000 SNPs.

I assume you were able to create the Plink files from the Reich dataset based on the par file I wrote you. Can you post the plink .log file. It'll help me diagnose a few things.

Assuming you were able to get 1240K SNPs in your Plink data you can get about 70,000 overlapping SNPs if you only use your data and the Simmons samples in the Reich dataset. You'll recognize them because their IDs start with S_ such as "S_Armenian-1.DG"

If you only use your personal file and the Simmons ones starting in S_ when you extract in Admixtools 2 using:

extract_f2(pref, f2dir, pops = c(

then you should end up with about 70,000 SNPs

**Zoro** · 03-02-2021, 05:34 PM

Originally Posted by Kaspias

First run:

√ 1379990 SNPs read in total
! 6558 SNPs remain after filtering. 6468 are polymorphic.

Code:

 target      left      weight     se     z
                  
1 Kaspias Turkmen    0.164 0.0991  1.65
2 Kaspias Bulgarian  0.836 0.0991  8.44

Many thanks to @Korialstrasz for the tutorial also to @vbnetkhio and @Zoro for giving a hand. I'd like to see some feedback on it, so I can try to improve.

Congrats on making Plink files and using Admixtools. It's your gateway to much more meaningful analysis than merely using Vahaduo all the time !

6558 SNPs is too low to do an accurate comparison. Even though you weren't WGS genotyped I can still get you up to about 200,000 SNPs.

I assume you were able to create the Plink files from the Reich dataset based on the par file I wrote you. Can you post the plink .log file. It'll help me diagnose a few things.

Assuming you were able to get 1240K SNPs in your Plink data you can get about 200,000 overlapping SNPs if you only use your data and the Simmons samples in the Reich dataset. You'll recognize them because their IDs start with S_ such as "S_Armenian-1.DG"

If you only use your personal file and the Simmons ones starting in S_ when you extract in Admixtools 2 using:

extract_f2(pref, f2dir, pops = c(

then you should end up with about 200,000 SNPs

**Zoro** · 03-02-2021, 05:41 PM

I use Admixtools 2 based on Eigenstrat geno snp and ind files.

Here are some 1240K pops I use alot because they don't drop your SNP counts

extract_f2(pref, f2dir, pops = c('Eskimo_Sireniki.DG',
'Punjabi',
'Turkmen','Pathan','Kalash','Bashkir','Kotias',
'Tatar_Volga','Turkish','Iranian','Armenian',
'Saami','Georgian','Jordanian',
'Estonian','Bulgarian','Sardinian','Avar','Hazara' ,
'Khomani_San',
'Papuan',
'Chukchi','Han','Uyghur','Mansi',
'Mongola','Buryat','Yakut','Adygei','Burmese','Jew _Iraqi',
'Russia_Abkhasian',
'Karelia','Balochi','Brahui'), maxmiss=0,verbose=TRUE)

**Zoro** · 03-02-2021, 05:43 PM

.......

**Kaspias** · 03-02-2021, 07:30 PM

Originally Posted by Zoro

Congrats on making Plink files and using Admixtools. It's your gateway to much more meaningful analysis than merely using Vahaduo all the time !

6558 SNPs is too low to do an accurate comparison. Even though you weren't WGS genotyped I can still get you up to about 200,000 SNPs.

I assume you were able to create the Plink files from the Reich dataset based on the par file I wrote you. Can you post the plink .log file. It'll help me diagnose a few things.

Assuming you were able to get 1240K SNPs in your Plink data you can get about 200,000 overlapping SNPs if you only use your data and the Simmons samples in the Reich dataset. You'll recognize them because their IDs start with S_ such as "S_Armenian-1.DG"

If you only use your personal file and the Simmons ones starting in S_ when you extract in Admixtools 2 using:

extract_f2(pref, f2dir, pops = c(

then you should end up with about 200,000 SNPs

Log:

Code:

.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (960586 variants, 1 person).
--file: Kaspias_n-temporary.bed + Kaspias_n-temporary.bim +
Kaspias_n-temporary.fam written.
960586 variants loaded from .bim file.
1 person (0 males, 0 females, 1 ambiguous) loaded from .fam.
Ambiguous sex ID written to Kaspias_n.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 0 founders and 1 nonfounder present.
Calculating allele frequencies... done.
Total genotyping rate is 0.974373.
960586 variants and 1 person pass filters and QC.
Note: No phenotypes present.
--make-bed to Kaspias_n.bed + Kaspias_n.bim + Kaspias_n.fam ... done.

For merging:

Code:

54 people loaded from master_plink.fam.
1 person to be merged from Kaspias_n.fam.
Of these, 1 is new, while 0 are present in the base dataset.
597573 markers loaded from master_plink.bim.
960586 markers to be merged from Kaspias_n.bim.
Of these, 782417 are new, while 178169 are present in the base dataset.
Warning: Variants 'rs144847714' and 'rs10492943' have the same position.
Warning: Variants 'rs3205229' and 'rs2229002' have the same position.
Warning: Variants 'rs769902' and 'rs201435286' have the same position.
748 more same-position warnings: see log file.
Performing single-pass merge (55 people, 1379990 variants).
Merged fileset written to merged_data-merge.bed + merged_data-merge.bim +
merged_data-merge.fam .
1379990 variants loaded from .bim file.
55 people (0 males, 0 females, 55 ambiguous) loaded from .fam.
Ambiguous sex IDs written to merged_data.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 54 founders and 1 nonfounder present.
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.
Total genotyping rate is 0.432004.
1379990 variants and 55 people pass filters and QC.
Note: No phenotypes present.
--make-bed to merged_data.bed + merged_data.bim + merged_data.fam ... done.

**Kaspias** · 03-02-2021, 07:51 PM

Here it is...

√ 1379990 SNPs read in total
! 173175 SNPs remain after filtering. 170906 are polymorphic.

Code:

target      left         weight     se     z
                     
1 Kaspias Bulgarian.DG  0.776 0.0339 22.9 
2 Kaspias Turkmen.SG    0.224 0.0339  6.60

Code:

  target      left         weight     se     z
                     
1 Kaspias Bulgarian.DG  0.798 0.0299 26.7 
2 Kaspias Uzbek.SG      0.202 0.0299  6.76

**Zoro** · 03-02-2021, 08:03 PM

Originally Posted by Kaspias

Log:

Code:

.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (960586 variants, 1 person).
--file: Kaspias_n-temporary.bed + Kaspias_n-temporary.bim +
Kaspias_n-temporary.fam written.
960586 variants loaded from .bim file.
1 person (0 males, 0 females, 1 ambiguous) loaded from .fam.
Ambiguous sex ID written to Kaspias_n.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 0 founders and 1 nonfounder present.
Calculating allele frequencies... done.
Total genotyping rate is 0.974373.
960586 variants and 1 person pass filters and QC.
Note: No phenotypes present.
--make-bed to Kaspias_n.bed + Kaspias_n.bim + Kaspias_n.fam ... done.

For merging:

Code:

54 people loaded from master_plink.fam.
1 person to be merged from Kaspias_n.fam.
Of these, 1 is new, while 0 are present in the base dataset.
597573 markers loaded from master_plink.bim.
960586 markers to be merged from Kaspias_n.bim.
Of these, 782417 are new, while 178169 are present in the base dataset.
Warning: Variants 'rs144847714' and 'rs10492943' have the same position.
Warning: Variants 'rs3205229' and 'rs2229002' have the same position.
Warning: Variants 'rs769902' and 'rs201435286' have the same position.
748 more same-position warnings: see log file.
Performing single-pass merge (55 people, 1379990 variants).
Merged fileset written to merged_data-merge.bed + merged_data-merge.bim +
merged_data-merge.fam .
1379990 variants loaded from .bim file.
55 people (0 males, 0 females, 55 ambiguous) loaded from .fam.
Ambiguous sex IDs written to merged_data.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 54 founders and 1 nonfounder present.
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.
Total genotyping rate is 0.432004.
1379990 variants and 55 people pass filters and QC.
Note: No phenotypes present.
--make-bed to merged_data.bed + merged_data.bim + merged_data.fam ... done.

Ok I see that you have 178k SNPs overlapping with master dataset. You can increase that quite a bit by using the Reich 1240K instead of the 593k set you are using. It’s available at Reich Lab.

You can easily convert it from Eigenstrat to plink using the par file I gave you

Then in Plink you can merge your personal data and any other data with it. You can do IBS analysis in plink

Then you can convert your new plink master back to Eigenstrat. Let me know when you’re ready I’ll give you a different par file to do that

Then you can do Admixtools with you included using Eigenstrat

**Zoro** · 03-02-2021, 08:08 PM

Originally Posted by Kaspias

Here it is...

√ 1379990 SNPs read in total
! 173175 SNPs remain after filtering. 170906 are polymorphic.

Code:

target      left         weight     se     z
                     
1 Kaspias Bulgarian.DG  0.776 0.0339 22.9 
2 Kaspias Turkmen.SG    0.224 0.0339  6.60

Code:

  target      left         weight     se     z
                     
1 Kaspias Bulgarian.DG  0.798 0.0299 26.7 
2 Kaspias Uzbek.SG      0.202 0.0299  6.76

Looking much better. Standard errors look good at 3%. Can you post the p-values so we can see if models are pass or fail. The 3rd row contains the p-value. Also can you post the p-right pops used