I am working with whole genome sequencing data. It is produced batch by batch at Illumina. Joint variant calling is done by one of my peers, she then gives me the resulting vcf file and I’m asked to check if we find any batch effect in our data.

PCA analysis on common SNP is an easy job. I wan’t to go further and use every SNPs: I am really interested in rare variants. I performed a « GWAS » where phenotypes are batch ID using PLINK’s --loop-assoc command.

I was asked to find another way to check batch effect. As I am a trained biostatistician, I don’t know how to do so and I struggle to find any litterature on software or anything in this optic. Is there anything someone with experience in this field can do for me regarding this?

Thank you.