ADNI DATASET

Question

[karthick]

I have GWAS analysis in the ADNI dataset (WGS CASAVA Illumina software dataset). I have GWAS analysis using the plink tool in QC, but alzheimer disease risk factor SNPs remove this QC step. Why? steps : I have an Alzheimer's disease dataset in VCF file format. In this vcf file, the last two columns are present in MAXGT and PLOY. In this two-column genotype information column, I have taken the MAXGT column only for GWAS analysis. Next, I have index and merge in bcftools. Convert vcf to plink format after merging.

QC steps:
--geno 0.2 and 0.02 this filter step alzheimer disease highly significant snp removed
--check-sex this step problem PEDSEX and SNPSEX this two are different
--mind 0.2&0.02
--maf 0.05
--hwe

what is problem ? i don't understand help me .

[karthick]

I am performing GWAS analysis on the ADNI dataset (WGS CASAVA Illumina dataset) using the PLINK tool for quality control (QC). However, Alzheimer's disease risk factor SNPs are being removed during the QC steps. I am unsure why this is happening.

Steps followed:

I have an Alzheimer's disease dataset in VCF file format. In the VCF file, the last two columns contain MAXGT and PLOY, representing genotype information. I used only the MAXGT column for GWAS analysis. I indexed and merged the VCF files using bcftools. I converted the merged VCF file into PLINK format. QC steps applied:

--geno 0.2 and 0.02: This filter removed highly significant SNPs associated with Alzheimer's disease.
--check-sex: There is a discrepancy between PEDSEX and SNPSEX, causing an issue.
--mind 0.2 and 0.02
--maf 0.05
--hwe