QTL data postprocessing

QTL data postprocessing#

To be updated, you can safely skip it for now.

Generate yml#

sos run xqtl-protocol/pipeline/yml_generator.ipynb yml_list \
    --sumstat-list /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/TADB/TensorQTL.cis._recipe.tsv \
    --cwd /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad \
    --name pQTL \
    --container /mnt/vast/hpc/csg/containers/bioinfo.sif

Generate the target#

sos run xqtl-protocol/pipeline/summary_stats_standardizer.ipynb TARGET_generation \
    --fasta /mnt/vast/hpc/csg/molecular_phenotype_calling/reference_data/GRCh38_full_analysis_set_plus_decoy_hla.noALT_noHLA_noDecoy_ERCC.fasta  \
    --sumstat-list /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/qced_sumstat_list.txt \
    --yml-list /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/yml_list.txt  \
    --cwd /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad \
    --container /mnt/vast/hpc/csg/containers/bioinfo.sif \
    --walltime 100h \
    --numThreads 20 \
    --mem 150G -J 50 -c /mnt/vast/hpc/csg/molecular_phenotype_calling/csg.yml -q csg

Standardized the sumstat#

sos run xqtl-protocol/pipeline/summary_stats_standardizer.ipynb sumstat_standardization \
    --sumstat-list /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/qced_sumstat_list.txt  \
    --yml-list /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/yml_list.txt \
    --TARGET_list /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/TARGET.ref.list \
    --cwd /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/ \
    --container /mnt/vast/hpc/csg/containers/bioinfo.sif \
    --walltime 100h \
    --numThreads 20 \
    --mem 200G -J 50 -c /mnt/vast/hpc/csg/molecular_phenotype_calling/csg.yml -q csg

Convert sumstats to VCF#

sos run xqtl-protocol/pipeline/summary_stats_standardizer.ipynb sumstat_to_vcf \
    --sumstat-list /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/qced_sumstat_list.txt  \
    --cwd /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/ \
    --container /mnt/vast/hpc/csg/containers/bioinfo.sif \
    --walltime 100h \
    --numThreads 20 \
    --mem 200G -J 50 -c /mnt/vast/hpc/csg/molecular_phenotype_calling/csg.yml -q csg

Associate result processing#

sos run xqtl-protocol/pipeline/assoc_result_processing.ipynb genome \
    --vcf `ls /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/*/*cis_long_table.vcf` \
    --padjust-method "bonferroni" \
    --container /mnt/vast/hpc/csg/containers/bioinfo.sif \
    --mem 200G -J 22 -q csg -c /mnt/vast/hpc/csg/molecular_phenotype_calling/csg.yml

Summary of result - To be update#

cat /mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/rosmap_stad/pQTL.1/pheno_recipe_rosmap_pheno.rosmap_cov.ROSMAP_NIA_WGS.leftnorm.filtered.pQTL.unrelated.filtered.prune.pca.resid.Marchenko_pc.1.n_sig.txt

tissue

n_assoc

n_snp

n_gene

pQTL

290330

266394

3166
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