Knight ADRC brain proteomics QTL #
Charles F. And Joanne Knight Alzheimer’s Disease Research Center (Knight-ADRC) Please refer to this document for an overview of the Knight project.
Contact #
Zining Qi( zq2209@cumc.columbia.edu)
Study Overview #
- Study name : Knight ADRC brain proteomics QTL
- Study Description : Charles F. And Joanne Knight Alzheimer’s Disease Research Center (Knight-ADRC) brain proteomics QTL analysis summary statistics using the FGC xQTL pipeline. Samples' phenotype information (sex, age, race etc.) can be found in Knight metadata, see “Other information” section in this document
Analysis Status #
TransQTL association: Need to be updated with new covariate files.
Analysis Details #
Sample size tracking through the analysis workflow #
| Step | Sample Size |
|---|---|
| Raw data | 442 |
| After overlapping with Knight covariates | 418 |
| After overlapping with Knight genotype | 412 |
QC and Normalization Details for Phenotype Data #
For QCs performed on data please refer to descriptor/omics/Knight_ADRC_brain_proteomics.md
Genotype parameters #
- Kinship coefficient for related individuals: 0.0625
- Minor allele count cutoff for single variant analysis: 5
- Variant level missingness threshold: 0.1
- Sample level missingness threshold: 0.1
Covariate parameters #
PCA analysis:
- MAF for PCA: 0.05
- LD pruning via PLINK for PCA analysis: window 50, shift 10, r2 0.1
- Tolerance of missingness in covariates: 0.3
- number of pc that captured more than 70% PVE were kept Hidden Factor analysis - PCA
- Use Marchenko-Pastur limit to choose PCs Final covariates: Sex, Age at death, PMI, PCs(12), hidden factors(18)
TensorQTL association scan parameters #
- cis/trans window for the up and downstream radius to analyze around the region of interest, in units of bp: 1000000
- Minor allele count cutoff: 5
- Minor allele frequency cutoff: 5/(2.0*592) = 0.00422297
Links to QTL analysis notebooks #
See notebooks in:
- https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Wang_Columbia/knight/pqtl The notebooks in this folder contain the commands and data wrangling codes for analysis of the proteomics data in ROSMAP. (data wrangling exist because not all data are processed using the xqtl-pipeline from the begnning and need to be reformated to fit one intermediate step of the pipeline).
Association data preprocessing #
phenotype preprocessing can be run in parallel but covariate preprocessing need to be done last since it requires both phenotype data and PCs from PCA in genotype preprocessing.
- genotype_preprocessing.ipynb shows the commands used for genotype processing and preparation steps.
- Includes QC, PCA, and PCA result figures.
- phenotype_preprocessing.ipynb shows the commands used for the phenotype data processing and preparation steps.
- This notebook strated from some already cleaned data and covert them to bed format inputs taken by tensorQTL.
- covariate_preprocessing.ipynb shows the commands used for the covariate data processing and preparation steps.
- This includes PCA hidden factor analysis steps and merging the PCA hidden factors to covariates and PCA.
Association scan using TensorQTL and summary statistics standardization #
- cis_pqtl_association.ipynb provides information and result of cis-QTL analysis.
- trans_pqtl_association.ipynb provides information and result of AD genes trans-QTL analysis.
Dataset Description #
Path(s) to genotype matrix #
- Wang Lab,
/mnt/vast/hpc/csg/molecular_phenotype_calling/WashU_genotype/genotype_qc
-rw-r--r-- 1 zq2209 zq2209 48M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.10.bed
-rw-r--r-- 1 zq2209 zq2209 17M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.10.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.10.fam
-rw-r--r-- 1 zq2209 zq2209 47M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.11.bed
-rw-r--r-- 1 zq2209 zq2209 16M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.11.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.11.fam
-rw-r--r-- 1 zq2209 zq2209 45M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.12.bed
-rw-r--r-- 1 zq2209 zq2209 16M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.12.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.12.fam
-rw-r--r-- 1 zq2209 zq2209 35M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.13.bed
-rw-r--r-- 1 zq2209 zq2209 12M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.13.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.13.fam
-rw-r--r-- 1 zq2209 zq2209 30M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.14.bed
-rw-r--r-- 1 zq2209 zq2209 11M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.14.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.14.fam
-rw-r--r-- 1 zq2209 zq2209 26M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.15.bed
-rw-r--r-- 1 zq2209 zq2209 8.9M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.15.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.15.fam
-rw-r--r-- 1 zq2209 zq2209 29M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.16.bed
-rw-r--r-- 1 zq2209 zq2209 9.6M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.16.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.16.fam
-rw-r--r-- 1 zq2209 zq2209 25M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.17.bed
-rw-r--r-- 1 zq2209 zq2209 8.3M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.17.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.17.fam
-rw-r--r-- 1 zq2209 zq2209 27M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.18.bed
-rw-r--r-- 1 zq2209 zq2209 9.1M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.18.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.18.fam
-rw-r--r-- 1 zq2209 zq2209 21M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.19.bed
-rw-r--r-- 1 zq2209 zq2209 7.0M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.19.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.19.fam
-rw-r--r-- 1 zq2209 zq2209 72M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.1.bed
-rw-r--r-- 1 zq2209 zq2209 24M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.1.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.1.fam
-rw-r--r-- 1 zq2209 zq2209 21M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.20.bed
-rw-r--r-- 1 zq2209 zq2209 7.0M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.20.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.20.fam
-rw-r--r-- 1 zq2209 zq2209 13M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.21.bed
-rw-r--r-- 1 zq2209 zq2209 4.3M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.21.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.21.fam
-rw-r--r-- 1 zq2209 zq2209 13M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.22.bed
-rw-r--r-- 1 zq2209 zq2209 4.3M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.22.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.22.fam
-rw-r--r-- 1 zq2209 zq2209 77M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.2.bed
-rw-r--r-- 1 zq2209 zq2209 26M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.2.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.2.fam
-rw-r--r-- 1 zq2209 zq2209 66M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.3.bed
-rw-r--r-- 1 zq2209 zq2209 22M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.3.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.3.fam
-rw-r--r-- 1 zq2209 zq2209 68M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.4.bed
-rw-r--r-- 1 zq2209 zq2209 23M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.4.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.4.fam
-rw-r--r-- 1 zq2209 zq2209 61M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.5.bed
-rw-r--r-- 1 zq2209 zq2209 20M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.5.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.5.fam
-rw-r--r-- 1 zq2209 zq2209 62M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.6.bed
-rw-r--r-- 1 zq2209 zq2209 21M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.6.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.6.fam
-rw-r--r-- 1 zq2209 zq2209 55M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.7.bed
-rw-r--r-- 1 zq2209 zq2209 18M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.7.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.7.fam
-rw-r--r-- 1 zq2209 zq2209 51M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.8.bed
-rw-r--r-- 1 zq2209 zq2209 17M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.8.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.8.fam
-rw-r--r-- 1 zq2209 zq2209 41M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.9.bed
-rw-r--r-- 1 zq2209 zq2209 14M Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.9.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.9.fam
-rw-r--r-- 1 zq2209 zq2209 922M Feb 14 10:37 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.bed
-rw-r--r-- 1 zq2209 zq2209 309M Feb 14 10:37 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:30 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.fam
-rw-r--r-- 1 zq2209 zq2209 19K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.X.bed
-rw-r--r-- 1 zq2209 zq2209 6.2K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.X.bim
-rw-r--r-- 1 zq2209 zq2209 9.4K Feb 14 17:36 MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.X.fam
Path(s) to omics-data matrix #
- Wang Lab,
/mnt/vast/hpc/csg/zq2209/data_production/proteomics/knight/pheno
$ ls -lh *.{txt,gz}
-rw-r--r-- 1 zq2209 zq2209 4.2M Jun 1 13:18 WashU_pheno.bed.gz
-rw-r--r-- 1 zq2209 zq2209 133K Jun 1 13:18 WashU_pheno_chr10.bed.gz
-rw-r--r-- 1 zq2209 zq2209 243K Jun 1 13:18 WashU_pheno_chr11.bed.gz
-rw-r--r-- 1 zq2209 zq2209 284K Jun 1 13:18 WashU_pheno_chr12.bed.gz
-rw-r--r-- 1 zq2209 zq2209 83K Jun 1 13:18 WashU_pheno_chr13.bed.gz
-rw-r--r-- 1 zq2209 zq2209 122K Jun 1 13:18 WashU_pheno_chr14.bed.gz
-rw-r--r-- 1 zq2209 zq2209 111K Jun 1 13:18 WashU_pheno_chr15.bed.gz
-rw-r--r-- 1 zq2209 zq2209 144K Jun 1 13:18 WashU_pheno_chr16.bed.gz
-rw-r--r-- 1 zq2209 zq2209 291K Jun 1 13:18 WashU_pheno_chr17.bed.gz
-rw-r--r-- 1 zq2209 zq2209 57K Jun 1 13:18 WashU_pheno_chr18.bed.gz
-rw-r--r-- 1 zq2209 zq2209 348K Jun 1 13:18 WashU_pheno_chr19.bed.gz
-rw-r--r-- 1 zq2209 zq2209 453K Jun 1 13:18 WashU_pheno_chr1.bed.gz
-rw-r--r-- 1 zq2209 zq2209 151K Jun 1 13:18 WashU_pheno_chr20.bed.gz
-rw-r--r-- 1 zq2209 zq2209 91K Jun 1 13:18 WashU_pheno_chr21.bed.gz
-rw-r--r-- 1 zq2209 zq2209 103K Jun 1 13:18 WashU_pheno_chr22.bed.gz
-rw-r--r-- 1 zq2209 zq2209 238K Jun 1 13:18 WashU_pheno_chr2.bed.gz
-rw-r--r-- 1 zq2209 zq2209 220K Jun 1 13:18 WashU_pheno_chr3.bed.gz
-rw-r--r-- 1 zq2209 zq2209 235K Jun 1 13:18 WashU_pheno_chr4.bed.gz
-rw-r--r-- 1 zq2209 zq2209 222K Jun 1 13:18 WashU_pheno_chr5.bed.gz
-rw-r--r-- 1 zq2209 zq2209 177K Jun 1 13:18 WashU_pheno_chr6.bed.gz
-rw-r--r-- 1 zq2209 zq2209 182K Jun 1 13:18 WashU_pheno_chr7.bed.gz
-rw-r--r-- 1 zq2209 zq2209 129K Jun 1 13:18 WashU_pheno_chr8.bed.gz
-rw-r--r-- 1 zq2209 zq2209 138K Jun 1 13:18 WashU_pheno_chr9.bed.gz
-rw-r--r-- 1 zq2209 zq2209 115K Jun 1 13:18 WashU_pheno_chrX.bed.gz
Path(s) to covariate data matrix #
- Wang Lab,
/mnt/vast/hpc/csg/zq2209/data_production/proteomics/knight/cov
$ ls -lh *.gz
-rw-r--r-- 1 zq2209 zq2209 113K Jun 1 13:22 WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.gz
Path(s) to QTL results #
- Wang lab:
/mnt/vast/hpc/csg/molecular_phenotype_calling/pQTL_cis/WashU
ls -lh *.txt
-rw-r--r-- 1 zq2209 zq2209 8.9K May 19 14:33 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.10.emprical.cis_sumstats.txt
-rw-r--r-- 1 zq2209 zq2209 44M May 19 14:32 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.10.norminal.cis_long_table.txt
-rw-r--r-- 1 zq2209 zq2209 17K May 19 14:34 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.11.emprical.cis_sumstats.txt
-rw-r--r-- 1 zq2209 zq2209 76M May 19 14:34 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.11.norminal.cis_long_table.txt
-rw-r--r-- 1 zq2209 zq2209 19K May 19 14:36 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.12.emprical.cis_sumstats.txt
-rw-r--r-- 1 zq2209 zq2209 81M May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.12.norminal.cis_long_table.txt
-rw-r--r-- 1 zq2209 zq2209 5.5K May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.13.emprical.cis_sumstats.txt
-rw-r--r-- 1 zq2209 zq2209 26M May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.13.norminal.cis_long_table.txt
-rw-r--r-- 1 zq2209 zq2209 8.6K May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.14.emprical.cis_sumstats.txt
-rw-r--r-- 1 zq2209 zq2209 41M May 19 14:34 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.14.norminal.cis_long_table.txt
-rw-r--r-- 1 zq2209 zq2209 7.2K May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.15.emprical.cis_sumstats.txt
-rw-r--r-- 1 zq2209 zq2209 29M May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.15.norminal.cis_long_table.txt
-rw-r--r-- 1 zq2209 zq2209 9.8K May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.16.emprical.cis_sumstats.txt
-rw-r--r-- 1 zq2209 zq2209 42M May 19 14:35 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.16.norminal.cis_long_table.txt
-rw-r--r-- 1 zq2209 zq2209 20K May 19 14:37 pheno_recipe_WashU_pheno.WashU_cov.MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.filtered.pQTL.related.filtered.extracted.pca.projected.resid.Marchenko_pc.17.emprical.cis_sumstats.txt
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