Hi,
When I use eqtlbma_bf, I found that it loaded keep no SNP from vcf file. My vcf file didn't contatin any SNPs with missing genotypes because I already filtered before. So I wonder what caused this.
Here is my commond and outputs of eqtlbam_bf.
eqtlbma_bf --geno list_genotypes.txt --exp list_explevels.txt --gcoord gene_coords.bed.gz --anchor TSS --cis 1000000 --out out_eqtlbma --analys join --covar list_covariates.txt --gridL grid_phi2_oma2_general.txt --gridS grid_phi2_oma2_with-configs.txt --bfs all --error mvlr --thread=4
load file list_explevels.txt ...
items loaded: 2
load file list_genotypes.txt ...
items loaded: 2
load file list_covariates.txt ...
items loaded: 2
analyze 2 subgroups (identifier):
Normal (1)
Tumor (2)
load samples ...
nb of samples (explevels): 268
Normal: 134 samples
Tumor: 134 samples
nb of samples (genotypes): 134
Normal: 134 samples
Tumor: 134 samples
total nb of samples: 268
nb of samples (covariates): 134
Normal: 134 samples
Tumor: 134 samples
load covariates ...
Normal (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Covariates_normal.txt.gz): 21 covariates
Tumor (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Covariates_tumor.txt.gz): 22 covariates
load gene coordinates ...
total nb of genes with coordinates: 35252
load gene expression levels ...
Normal (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Expression_normalization_normal.txt.gz): 35252 genes (to keep: 35252)
Tumor (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Expression_normalization_tumor.txt.gz): 35252 genes (to keep: 35252)
total nb of genes to analyze: 35252
load genotypes and SNP coordinates ...
Normal (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/combined.134.nomiss.recode.vcf.gz): 5444712 SNPs (to keep: 0, loaded in 111.38 sec)
discard SNPs with missing values ...
duplicate genotypes for other subgroups (same file) ...
Tumor (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/combined.134.nomiss.recode.vcf.gz): 0 SNPs duplicated in 0.00 sec
nb of SNPs: 0
END lt-eqtlbma_bf 2023-03-16 21:11:55
elapsed -> 0d 0h 1m 59s
max.mem -> 100732 kB
Hi, When I use eqtlbma_bf, I found that it loaded keep no SNP from vcf file. My vcf file didn't contatin any SNPs with missing genotypes because I already filtered before. So I wonder what caused this. Here is my commond and outputs of eqtlbam_bf.