Hello,

I am trying to impute the genotypes of 32 individuals to WGS with Beagle 5.4 and I found inconsistences between beagle logs and my SNP data. I run Beagle with this:

java -Xss51m -Xmx64g -jar beagle.22Jul22.46e.jar gt=genotype_Chr1.vcf ref=training_ref_Chr1.vcf.gz out=genotypeChr1_imputed

These are the first lines of the log:

No genetic map is specified: using 1 cM = 1 Mb

Reference samples:                1,842
Study     samples:                   32

Window 1 [1:695-40000660]
Reference markers:            2,304,542
Study     markers:                    4

Which makes no sense since in my SNP data (genotype_Chr1.vcf) there are more than 4 SNPs in the 1:695-40000660 window. Here are the first lines of the corresponding .bim file :

1   Hapmap43437-BTA-101873  0   135098  G   A
1   ARS-BFGL-NGS-16466  0   267940  A   G
1   EuroGMD_SNP_BTA1_rs110119084    0   349826  A   G
1   EuroGMD_SNP_BTA1_rs41567297 0   351236  A   G
1   EuroGMD_SNP_BTA1_rs109566607    0   351516  A   C
1   EuroG10K_ARS-BFGL-NGS-105096    0   353745  A   G
1   Hapmap34944-BES1_Contig627_1906 0   393248  A   C

Is this supposed to happen? Why is Beagle only using 4 of the hundreds/thousands of markers present in this window? I'm fairly new to beagle, so I do not know if I'm doing something wrong.

Thanks