Wrong results?

[mcetincompbio]

I ran this command:
/usr/local/softw/NgsRelate/ngsRelate -h input.vcf -T GT -O results.res -c 1

Here is the relevant part of the result

a b nSites J9 J8 J7 J6 J5 J4 J3 J2 J1 rab Fa Fb theta inbred_relatedness_1_2 inbred_relatedness_2_1 fraternity identity zygosity 2of3_IDB FDiff loglh nIter coverage 2dsfs R0 R1 KING 2dsfs_loglike 2dsfsf_niter

100 101 26688 0.154319 0.125469 0.000000 0.016806 0.092420 0.000582 0.102905 0.000000 0.507499 0.716727 0.610986 0.616725 0.636528 0.558951 0.553709 0.000000 0.507499 0.507499 0.774252 -0.008112 -44505.357314 5000 0.323738 5.113872e-01,5.571375e-02,1.177190e-02,5.602682e-02,6.669632e-02,6.594131e-02,1.065887e-02,6.341072e-02,1.583932e-01 0.336312 0.253095 0.058306 -42959.275380 10

indiv.s 100 and 101 are siblings. Theoretically, for a sibling pair I would expect k0=0.25, k1=0.5, k2=0.25

However that is not what I see. Similarly for theta, which should be 0.25 but calculated as 0.636528.

Can you please help?

I tried -i 10000 but didn't help.

Thanks a lot.

[ANGSD]

Are the samples from one homogenous population or is there somekind of population structure?

…

On 19 Apr 2019, at 14.24, mcetincompbio ***@***.***> wrote: I ran this command: /usr/local/softw/NgsRelate/ngsRelate -h input.vcf -T GT -O results.res -c 1 Here is the result a b nSites J9 J8 J7 J6 J5 J4 J3 J2 J1 rab Fa Fb theta inbred_relatedness_1_2 inbred_relatedness_2_1 fraternity identity zygosity 2of3_IDB FDiff loglh nIter coverage 2dsfs R0 R1 KING 2dsfs_loglike 2dsfsf_niter 100 101 26688 0.154319 0.125469 0.000000 0.016806 0.092420 0.000582 0.102905 0.000000 0.507499 0.716727 0.610986 0.616725 0.636528 0.558951 0.553709 0.000000 0.507499 0.507499 0.774252 -0.008112 -44505.357314 5000 0.323738 5.113872e-01,5.571375e-02,1.177190e-02,5.602682e-02,6.669632e-02,6.594131e-02,1.065887e-02,6.341072e-02,1.583932e-01 0.336312 0.253095 0.058306 -42959.275380 10 indiv.s 100 and 101 are siblings. Theoretically, for a sibling pair I would expect k0=0.25, k1=0.5, k2=0.25 However that is not what I see. Similarly for theta, which should be 0.25 but calculated as 0.636528. Can you please help? I tried -i 10000 but didn't help. Thanks a lot. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#19>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABQOR3WK6WSCGMBQY6QBZUTPRG2YXANCNFSM4HHD2GDQ>.

[KHanghoj]

How does a PCA of the entire VCF file look like?

[mcetincompbio]

Are the samples from one homogenous population or is there somekind of population structure?

The samples are from the 1000 Genomes CEU population. I believe it should be somewhat homogenous.

How does a PCA of the entire VCF file look like?

The vcf file contains nearly 100 CEU individuals + 5 samples that also come from the same region.

I haven't drawn the PCA (sorry!), but for a PCA of the CEU population (together with others):

https://www.nature.com/articles/ejhg2017130/figures/1

[mcetincompbio]

I actually used SNPS with a maf above 0.45 (high!). I will check if that might be the issue and let you know, inş.