Dodecad k12b West & Central Asian results Vol 4.

[Sterling Archer]

Interesting but it seems Circassians are more aware of their origins and preserved it much better than Dagestanis and Chechens.

Do you think this might have been due to the fact that the Circassian migration was more wide scale? Bigger communities probably have much higher change of forming close-knit societies and retain cultural and ethnic identity.

[RatCat]

Do you think this might have been due to the fact that the Circassian migration was more wide scale? Bigger communities probably have much higher change of forming close-knit societies and retain cultural and ethnic identity.

It could be but in that article it says North Caucasians living in Iraq are actually %75 Chechen/Dagestani origin.

"According to the information obtained from North Caucasians in Iraq, it might be suggested that Chechens in Iraq composes approximately 75 percent of North Caucasian population. "

There are 1890 listed North Caucasian families settled in Iraq and 1300-1400 of them have Chechen and Dagestani origins and rest of them are Adyghe.

[RatCat]

double post

[Kaspias]

Actually I ran it using Plink. Here are the steps:

1- Make 2 column ( POP ID) text file of the good samples you want to use in the run, C.txt: ..../plink --bfile MASTER9 --keep C.txt --make-bed --out IBS

2- Use only SNPs overlapping in all samples: /plink --bfile IBS --geno 0.001 --make-bed --out IBS1

3- Calculate IBS using "genome" flag : /plink --bfile IBS1 --genome

4- Your results will be in folder plink.genome

It was helpful, thank you.

! 575774 SNPs remain after filtering. 552142 are polymorphic.

[Zoro]

It was helpful, thank you.

! 575774 SNPs remain after filtering. 552142 are polymorphic.

Great! If you want to filter out very old alleles common to all populations just repeat all the steps except this time do

/plink --bfile IBS --geno 0.001 --max-maf 0.30 --make-bed --out IBS1

This will filter out all minor alleles with frequency greater than 30% in IBS. You'll lose some SNPs but that's ok. The order of the pops will change a little based on more recent ancestry

[Kaspias]

Great! If you want to filter out very old alleles common to all populations just repeat all the steps except this time do

/plink --bfile IBS --geno 0.001 --max-maf 0.30 --make-bed --out IBS1

This will filter out all minor alleles with frequency greater than 30% in IBS. You'll lose some SNPs but that's ok. The order of the pops will change a little based on more recent ancestry

I think something is wrong here or am I interpreting wrong?

[Leto]

Can you guys stop posting that irrelevant stuff? I understand jack shit about those tables. You can call me stupid but if it ain't Gedmatch or G25, it's basically all Greek to me.

[Zoro]

I think something is wrong here or am I interpreting wrong?

1- How many SNPs did you end up with in Plink?
2- Do /plink --bfile IBS1 --missing and tell me if any samples have missing SNPs in plink.imiss

[Kaspias]

1- How many SNPs did you end up with in Plink?
2- Do /plink --bfile IBS1 --missing and tell me if any samples have missing SNPs in plink.imiss

1-

50 people (0 males, 0 females, 50 ambiguous) loaded from .fam.
Ambiguous sex IDs written to IBS1.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 49 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 0.757664.
1032168 variants removed due to missing genotype data (--geno).
192952 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
353388 variants and 50 people pass filters and QC.
Note: No phenotypes present.
--make-bed to IBS1.bed + IBS1.bim + IBS1.fam ... done.

2-

                   FID                     IID MISS_PHENO   N_MISS   N_GENO   F_MISS
           Kaspias_FAM                 Kaspias          Y        0   353388        0
           Albanian.DG         S_Albanian-1.DG          Y        0   353388        0
            Altaian.DG          S_Altaian-1.DG          Y        0   353388        0
  Anatolian_Turkish.DG          S_Turkish-1.DG          Y        0   353388        0
  Anatolian_Turkish.DG          S_Turkish-2.DG          Y        0   353388        0
           Armenian.DG         S_Armenian-1.DG          Y        0   353388        0
           Armenian.DG         S_Armenian-2.DG          Y        0   353388        0
            Bashkir.SG            Bashkirs1.SG          Y        0   353388        0
            Bashkir.SG            Bashkirs3.SG          Y        0   353388        0
          Bulgarian.DG        S_Bulgarian-1.DG          Y        0   353388        0
          Bulgarian.DG        S_Bulgarian-2.DG          Y        0   353388        0
             Cretan.DG            B_Crete-1.DG          Y        0   353388        0
             Cretan.DG            B_Crete-2.DG          Y        0   353388        0
     Eskimo_Chaplin.DG   S_Eskimo_Chaplin-1.DG          Y        0   353388        0
           Estonian.DG         S_Estonian-1.DG          Y        0   353388        0
           Estonian.DG         S_Estonian-2.DG          Y        0   353388        0
          Hungarian.DG        S_Hungarian-1.DG          Y        0   353388        0
          Hungarian.DG        S_Hungarian-2.DG          Y        0   353388        0
            Iranian.DG          S_Iranian-1.DG          Y        0   353388        0
            Iranian.DG          S_Iranian-2.DG          Y        0   353388        0
  Kyrgyz_Kyrgyzstan.DG           S_Kyrgyz-1.DG          Y        0   353388        0
  Kyrgyz_Kyrgyzstan.DG           S_Kyrgyz-2.DG          Y        0   353388        0
            Mongola.DG          S_Mongola-1.DG          Y        0   353388        0
            Mongola.DG          S_Mongola-2.DG          Y        0   353388        0
             Polish.DG           S_Polish-1.DG          Y        0   353388        0
            Russian.DG          S_Russian-1.DG          Y        0   353388        0
            Russian.DG          S_Russian-2.DG          Y        0   353388        0
              Saami.DG            S_Saami-1.DG          Y        0   353388        0
              Saami.DG            S_Saami-2.DG          Y        0   353388        0
          Sardinian.DG        B_Sardinian-3.DG          Y        0   353388        0
          Sardinian.DG        S_Sardinian-1.DG          Y        0   353388        0
          Sardinian.DG        S_Sardinian-2.DG          Y        0   353388        0
            S_Greek.DG            S_Greek-1.DG          Y        0   353388        0
            S_Greek.DG            S_Greek-2.DG          Y        0   353388        0
           S_Tuscan.DG           S_Tuscan-1.DG          Y        0   353388        0
           S_Tuscan.DG           S_Tuscan-2.DG          Y        0   353388        0
              Tajik.SG               Tadjik.SG          Y        0   353388        0
              Tajik.SG              Tajiks1.SG          Y        0   353388        0
              Tajik.SG              Tajiks3.SG          Y        0   353388        0
        Tatar_Tomsk.SG         TomskTatars1.SG          Y        0   353388        0
        Tatar_Tomsk.SG         TomskTatars2.SG          Y        0   353388        0
        Tatar_Volga.SG         VolgaTatars1.SG          Y        0   353388        0
        Tatar_Volga.SG         VolgaTatars2.SG          Y        0   353388        0
            Turkmen.SG            Turkmens1.SG          Y        0   353388        0
            Turkmen.SG            Turkmens2.SG          Y        0   353388        0
             Uyghur.DG            S_Uygur-1.DG          Y        0   353388        0
             Uyghur.DG            S_Uygur-2.DG          Y        0   353388        0
              Uzbek.SG              Uzbeks1.SG          Y        0   353388        0
              Uzbek.SG              Uzbeks2.SG          Y        0   353388        0
              Uzbek.SG              Uzbeks3.SG          Y        0   353388        0

[Zoro]

1-

50 people (0 males, 0 females, 50 ambiguous) loaded from .fam.
Ambiguous sex IDs written to IBS1.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 49 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 0.757664.
1032168 variants removed due to missing genotype data (--geno).
192952 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
353388 variants and 50 people pass filters and QC.
Note: No phenotypes present.
--make-bed to IBS1.bed + IBS1.bim + IBS1.fam ... done.

2-

                   FID                     IID MISS_PHENO   N_MISS   N_GENO   F_MISS
           Kaspias_FAM                 Kaspias          Y        0   353388        0
           Albanian.DG         S_Albanian-1.DG          Y        0   353388        0
            Altaian.DG          S_Altaian-1.DG          Y        0   353388        0
  Anatolian_Turkish.DG          S_Turkish-1.DG          Y        0   353388        0
  Anatolian_Turkish.DG          S_Turkish-2.DG          Y        0   353388        0
           Armenian.DG         S_Armenian-1.DG          Y        0   353388        0
           Armenian.DG         S_Armenian-2.DG          Y        0   353388        0
            Bashkir.SG            Bashkirs1.SG          Y        0   353388        0
            Bashkir.SG            Bashkirs3.SG          Y        0   353388        0
          Bulgarian.DG        S_Bulgarian-1.DG          Y        0   353388        0
          Bulgarian.DG        S_Bulgarian-2.DG          Y        0   353388        0
             Cretan.DG            B_Crete-1.DG          Y        0   353388        0
             Cretan.DG            B_Crete-2.DG          Y        0   353388        0
     Eskimo_Chaplin.DG   S_Eskimo_Chaplin-1.DG          Y        0   353388        0
           Estonian.DG         S_Estonian-1.DG          Y        0   353388        0
           Estonian.DG         S_Estonian-2.DG          Y        0   353388        0
          Hungarian.DG        S_Hungarian-1.DG          Y        0   353388        0
          Hungarian.DG        S_Hungarian-2.DG          Y        0   353388        0
            Iranian.DG          S_Iranian-1.DG          Y        0   353388        0
            Iranian.DG          S_Iranian-2.DG          Y        0   353388        0
  Kyrgyz_Kyrgyzstan.DG           S_Kyrgyz-1.DG          Y        0   353388        0
  Kyrgyz_Kyrgyzstan.DG           S_Kyrgyz-2.DG          Y        0   353388        0
            Mongola.DG          S_Mongola-1.DG          Y        0   353388        0
            Mongola.DG          S_Mongola-2.DG          Y        0   353388        0
             Polish.DG           S_Polish-1.DG          Y        0   353388        0
            Russian.DG          S_Russian-1.DG          Y        0   353388        0
            Russian.DG          S_Russian-2.DG          Y        0   353388        0
              Saami.DG            S_Saami-1.DG          Y        0   353388        0
              Saami.DG            S_Saami-2.DG          Y        0   353388        0
          Sardinian.DG        B_Sardinian-3.DG          Y        0   353388        0
          Sardinian.DG        S_Sardinian-1.DG          Y        0   353388        0
          Sardinian.DG        S_Sardinian-2.DG          Y        0   353388        0
            S_Greek.DG            S_Greek-1.DG          Y        0   353388        0
            S_Greek.DG            S_Greek-2.DG          Y        0   353388        0
           S_Tuscan.DG           S_Tuscan-1.DG          Y        0   353388        0
           S_Tuscan.DG           S_Tuscan-2.DG          Y        0   353388        0
              Tajik.SG               Tadjik.SG          Y        0   353388        0
              Tajik.SG              Tajiks1.SG          Y        0   353388        0
              Tajik.SG              Tajiks3.SG          Y        0   353388        0
        Tatar_Tomsk.SG         TomskTatars1.SG          Y        0   353388        0
        Tatar_Tomsk.SG         TomskTatars2.SG          Y        0   353388        0
        Tatar_Volga.SG         VolgaTatars1.SG          Y        0   353388        0
        Tatar_Volga.SG         VolgaTatars2.SG          Y        0   353388        0
            Turkmen.SG            Turkmens1.SG          Y        0   353388        0
            Turkmen.SG            Turkmens2.SG          Y        0   353388        0
             Uyghur.DG            S_Uygur-1.DG          Y        0   353388        0
             Uyghur.DG            S_Uygur-2.DG          Y        0   353388        0
              Uzbek.SG              Uzbeks1.SG          Y        0   353388        0
              Uzbek.SG              Uzbeks2.SG          Y        0   353388        0
              Uzbek.SG              Uzbeks3.SG          Y        0   353388        0

No of SNPs is ok and no samples have missing SNPs. Are you sure you converted your FTDNA data properly? If yes, then i suspect it’s ascertainment bias because the company that genotyped you used a drastically different set of SNPs than Simons. Too bad you don’t have WGS. Nebula or Sequencing.com does WGS for only like $79 it’s totally worth it for you to do it on yourself

For now disregard max-maf 0.3 to minimize bias


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