Discrodance between the Global Ancestry estimates using FLARE and ADMIXTURE and large estimate of Admixture time

Question

Discrodance between the Global Ancestry estimates using FLARE and ADMIXTURE and large estimate of Admixture time

Devashish13 opened this issue 2 years ago · 1 comments

Hi,
ABM_Flare_g70.out.log
ABM_Flare.out.log

I started implementing FLARE in Admixed Indian Subpopulations. Indian Populations are a result of complex admixture history of four ancestral populations Indo-European(IE), AustroAsiatic(AA), Dravidian(DR), Tibet-Berman(TB) speakers. The time since last admixture is around 70 generations as populations started endogamy.

By taking representative population for each of the four ancestral populations(having global ancestry~1) based on ADMIXTURE results and taking the Admixed populations data I am running FLARE.

Chromosome 21 has been taken to perform the analysis.

################## FLARE output #####################################
Model 1: Default Parameters

list of ancestries
IE DR AA TB

list of reference panels
IE DR AA TB

T: number of generations since admixture
1163.9318

mu[i]: proportion of target genotypes with ancestry i
1.0 0.0 0.0 0.0

p[i][j]: probability that a model state haplotype is in reference panel j when the model state ancestry is i
0.52692056 0.16545793 0.16131613 0.14630541
0.1464599 0.6767872 0.10465198 0.07210092
0.14689372 0.11054649 0.64248073 0.10007905
0.21040414 0.12552024 0.1592307 0.5048449

theta[i][j]: probability that a model state haplotype and the target haplotype carry different alleles when the model state haplotype is in reference panel j and the model state ancestry is i
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4

rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i
1257.5281 795.9301 783.3869 1147.2806

Model 2: gen=70,
list of ancestries
IE DR AA TB

list of reference panels
IE DR AA TB

T: number of generations since admixture
910.75415

mu[i]: proportion of target genotypes with ancestry i
1.0 0.0 0.0 0.0

p[i][j]: probability that a model state haplotype is in reference panel j when the model state ancestry is i
0.52692056 0.16545793 0.16131613 0.14630541
0.1464599 0.6767872 0.10465198 0.07210092
0.14689372 0.11054649 0.64248073 0.10007905
0.21040414 0.12552024 0.1592307 0.5048449

theta[i][j]: probability that a model state haplotype and the target haplotype carry different alleles when the model state haplotype is in reference panel j and the model state ancestry is i
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4
9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4

rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i
1257.5281 795.9301 783.3869 1147.2806

############## ADMIXTURE Global Ancestry for Admixed population taken under study

Ancestral_pop IE DR TB AA
Global Ancestry 0.26 0.3 0.18 0.26

I have also attached log files for your reference.

Please help me in understanding what is getting wrong here.

Thanks,
Devashish Tripathi

Answer 1 · 2022-08-26T23:27:02.000Z

Dear Devanish, Please send analysis related questions to Sharon ***@***.***). Sharon does not monitor this GitHub page. Please include the log file and output .model file from your analysis as e-mail attachments. Thanks, Brian Browning

…

On Fri, Aug 26, 2022 at 4:08 PM Devashish Tripathi ***@***.***> wrote: Hi, ABM_Flare_g70.out.log <https://github.com/browning-lab/flare/files/9436745/ABM_Flare_g70.out.log> ABM_Flare.out.log <https://github.com/browning-lab/flare/files/9436746/ABM_Flare.out.log> I started implementing FLARE in Admixed Indian Subpopulations. Indian Populations are a result of complex admixture history of four ancestral populations Indo-European(IE), AustroAsiatic(AA), Dravidian(DR), Tibet-Berman(TB) speakers. The time since last admixture is around 70 generations as populations started endogamy. By taking representative population for each of the four ancestral populations(having global ancestry~1) based on ADMIXTURE results and taking the Admixed populations data I am running FLARE. Chromosome 21 has been taken to perform the analysis. ################## *FLARE output* ##################################### *Model 1: Default Parameters* list of ancestries IE DR AA TB list of reference panels IE DR AA TB T: number of generations since admixture 1163.9318 mu[i]: proportion of target genotypes with ancestry i 1.0 0.0 0.0 0.0 p[i][j]: probability that a model state haplotype is in reference panel j when the model state ancestry is i 0.52692056 0.16545793 0.16131613 0.14630541 0.1464599 0.6767872 0.10465198 0.07210092 0.14689372 0.11054649 0.64248073 0.10007905 0.21040414 0.12552024 0.1592307 0.5048449 theta[i][j]: probability that a model state haplotype and the target haplotype carry different alleles when the model state haplotype is in reference panel j and the model state ancestry is i 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i 1257.5281 795.9301 783.3869 1147.2806 *Model 2: gen=70,* list of ancestries IE DR AA TB list of reference panels IE DR AA TB T: number of generations since admixture 910.75415 mu[i]: proportion of target genotypes with ancestry i 1.0 0.0 0.0 0.0 p[i][j]: probability that a model state haplotype is in reference panel j when the model state ancestry is i 0.52692056 0.16545793 0.16131613 0.14630541 0.1464599 0.6767872 0.10465198 0.07210092 0.14689372 0.11054649 0.64248073 0.10007905 0.21040414 0.12552024 0.1592307 0.5048449 theta[i][j]: probability that a model state haplotype and the target haplotype carry different alleles when the model state haplotype is in reference panel j and the model state ancestry is i 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i 1257.5281 795.9301 783.3869 1147.2806 ############## *ADMIXTURE Global Ancestry* for Admixed population taken under study Ancestral_pop IE DR TB AA Global Ancestry 0.26 0.3 0.18 0.26 I have also attached *log files* for your reference. Please help me in understanding what is getting wrong here. Thanks, Devashish Tripathi — Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKDWBPAT2SRLI2OJRCIKCWTV3FE7FANCNFSM57YH576A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>