Why many SNPs were excluded as invariant or singleton in population 2 ?

[yuan102379]

Hi hardingnj,

First, thanks a lot for your outstanding XP-CLR software.

Now, I have tried to employ XP-CLR to conduct selective sweep analysis. Howerver, I noticed that some SNPs were excluded as invariant or singleton in population 2, which were not used for the analysis. The log information is listed as follows:

####################
2020-06-21 11:32:38 : INFO : running xpclr v1.1.2
2020-06-21 11:32:38 : INFO : Loading TXT
2020-06-21 11:33:54 : INFO : TXT loading complete
2020-06-21 11:33:54 : INFO : 951,143 SNPs in total are in the provided input files
2020-06-21 11:33:54 : INFO : 0 SNPs excluded as multiallelic
2020-06-21 11:33:54 : INFO : 0 SNPs excluded as missing in all samples in a population
2020-06-21 11:33:54 : INFO : 62,460 SNPs excluded as invariant or singleton in population 2
2020-06-21 11:33:54 : INFO : 888,683/951,143 SNPs included in the analysis (93.43%)
2020-06-21 11:33:55 : INFO : Done dropping above SNPs from analysis. XP-CLR algorithm starting.
2020-06-21 11:33:56 : INFO : Omega estimated as : 0.655994
2020-06-21 11:33:56 : DEBUG : Processing window 1/5713...
2020-06-21 11:38:02 : DEBUG : Processing window 11/5713...
2020-06-21 11:41:45 : DEBUG : Processing window 21/5713...
2020-06-21 11:41:59 : DEBUG : Processing window 31/5713...

#####################

Could you give the reason for the the exclueded SNPs, please ? Where can I find the detail information of the excluded SNPs ? If these SNPs were specific in population 2, they should be important for the population 2. Were these SNPs were also filtered in the old XP-CLR program of Chen (2010) ?

Thanks for your help & have a nice day.

Yours,

Yuan

[hardingnj]

Hi there,

XPCLR is a 1 way scan. So, it's only looking for selection in population 1, not population 2. Think of them as object pop and reference pop. If you flip the populations (1->2, 2->1), then SNPs excluded from the first analysis may well be informative.

This isn't mentioned explicitly in the paper, but the likelihoods don't work if your reference population is fixed, as you have no way to drift to the value in pop1 under null assumption. You can drift from 0.5 to 0.0, but not 0.0 to 0.5.

Hope that helps.

[yuan102379]

Hi @hardingnj ,

Thanks for your outstanding explaining, which could help me to understand XPCLR a lot.

Can I have another question ?

I want to use map and geno files as the input files as same as the example data of Chen. However, In the map file, there were six column data. The thrid column is the genetic distance of SNP location. I want to make sure the unite of genetic distance. The unite is morgan or centi-mogran ? 1 morgan = 100 centi-mogran ?

Thanks a lot, hardingnj.

Yours,

Yuan

[hardingnj]

My apologies @yuan102379 - I missed your reply.

cM, so 1/100 of a Morgan. However, it's not important to the output because it's only used relatively within a window.