QTL Association Analysis

QTL Association Analysis#

This notebook contains the workflow to perform QTL association analysis.

Miniprotocol Timing#

This represents the total duration for all miniprotocol phases. While module-specific timings are provided separately on their respective pages, they are also included in this overall estimate.

Timing < X minutes

Overview#

This workflow is an application of the QTL association analysis from the xQTL project pipeline.

  1. TensorQTL.ipynb (step i, ii): run cis-QTL and trans-QTL analyses

Input#

  • output/genotype_by_chrom/protocol_example.genotype.chr21_22.genotype_by_chrom_files.txt: Generated from genotype_preprocessing

  • output/phenotype_by_chrom/protocol_example.protein.bed.phenotype_by_chrom_files.txt: Generated from phenotype_preprocessing

  • output/covariate/protocol_example.protein.protocol_example.samples.protocol_example.genotype.chr21_22.pQTL.unrelated.plink_qc.prune.pca.Marchenko_PC.gz: Generated from covariates_preprocessing

  • prototype_example/protocol_example/protocol_example.protein.enhanced_cis_chr21_chr22.bed: this is TAD-B list generated based on the TADB list TADB_enhanced_cis.bed to handle protein data. The code to generate it can be found in create_protocol_example_data. Please be noted that, all molecular_trait_id in the phenotype data are suppose to have a customized cis window corresponding to it.

Output#

  • Empirical cis results: /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap

  • Standardized cis results: /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/pQTL.#

Steps#

i. Cis TensorQTL Command#

sos run pipeline/TensorQTL.ipynb cis \
    --genotype-file output/genotype_by_chrom/wgs.merged.plink_qc.genotype_by_chrom_files.txt \
    --phenotype-file output/phenotype/phenotype_by_chrom/bulk_rnaseq.phenotype_by_chrom_files.txt \
    --covariate-file output/covariate/covariates.wgs.merged.plink_qc.plink_qc.prune.pca.gz \
    --customized-cis-windows reference_data/TAD/TADB_enhanced_cis.bed \
    --cwd output/tensorqtl_cis/ \
    --MAC 5

ii. Trans TensorQTL Command#

sos run pipeline/TensorQTL.ipynb trans \
    --genotype-file data/wgs.merged.plink_qc.genotype_trans_files.txt \
    --phenotype-file output/phenotype/phenotype_by_chrom_for_trans/bulk_rnaseq.phenotype_by_chrom_files.txt \
    --region-list data/combined_AD_genes.csv \
    --region-list-phenotype-column 4 \
    --covariate-file output/covariate/bulk_rnaseq_tmp_matrix.low_expression_filtered.outlier_removed.tmm.expression.covariates.wgs.merged.plink_qc.plink_qc.prune.pca.Marchenko_PC.gz \
    --cwd output/tensorqtl_trans/ \
    --MAC 5

Anticipated Results#

TensorQTL will produce empirical and standardized cis/trans results.

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