Hello everyone, I want to ask in order to do inverse quantile normalization using the gtex pipeline: https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl

eqtl_prepare_expression.py ${tpm_gct} ${counts_gct} ${annotation_gtf} \
    ${sample_participant_lookup} ${vcf_chr_list} ${prefix} \
    --tpm_threshold 0.1 \
    --count_threshold 6 \
    --sample_frac_threshold 0.2 \
    --normalization_method tmm

Can I follow this pipeline for normalization of gene counts for all the snps and not just eQTL. I am not able to understand at what step it specifically select eqtl for study. Can anyone please explain this part to me. Thank you.