├── README.md ├── code ├── 01-MungeData │ ├── HDBR_munge_metadata.R │ ├── Werling_munge_metadata.R │ ├── hdbr_concat_fastq.sh │ ├── libd_phase1_concat_fastq.sh │ ├── libd_phase2hippo_concat_fastq.sh │ ├── libd_phase2only_concat_fastq.sh │ ├── lists │ │ ├── hdbrOnly.exclude.mind.txt │ │ ├── hdbrOnlyFastqPrefix.txt │ │ ├── hdbrOnlyIndividual.txt │ │ ├── hdbrOnlySnpChip.txt │ │ ├── libd.1and2.subjects.txt │ │ ├── libd.1and2.subjects.withFamID.txt │ │ ├── libd.phase1.fastq.txt │ │ ├── libd.phase2hippo.fastq.txt │ │ ├── libd.phase2only.fastq.txt │ │ ├── obrienAndHDBRobrien.samples.txt │ │ ├── walker.txt │ │ ├── werling.fetal.samples.txt │ │ └── werling.geno.exclude.samples.txt │ └── plot_ancestry.R ├── 02-genotype │ ├── post-imputation │ │ ├── IBD.ipynb │ │ ├── Snakefile │ │ ├── ancestry.ipynb │ │ ├── checkVCF.py │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── ldstore │ │ │ ├── README │ │ │ ├── Snakefile │ │ │ ├── cluster_jobscript.sh │ │ │ ├── conditional_top_variants_table.txt │ │ │ └── snakemake.sh │ │ ├── locuszoom_ldfiles_biggerplot.ipynb │ │ ├── prelim │ │ │ ├── post-impute-01-concat-chr-hdbr.sh │ │ │ ├── post-impute-01-concat-chr-libd-1and2-1M.sh │ │ │ ├── post-impute-01-concat-chr-libd-1and2-h650.sh │ │ │ ├── post-impute-01-concat-chr-libd-2only-1M.sh │ │ │ ├── post-impute-01-concat-chr-libd-2only-h650.sh │ │ │ ├── post-impute-01-concat-chr-obrien.sh │ │ │ ├── post-impute-01-concat-chr-walker.sh │ │ │ ├── post-impute-01-concat-chr-werling.sh │ │ │ ├── post-impute-02-R2-filter-hdbr.sh │ │ │ ├── post-impute-02-R2-filter-libd.sh │ │ │ ├── post-impute-02-R2-filter-obrien.sh │ │ │ ├── post-impute-02-R2-filter-walker.sh │ │ │ ├── post-impute-02-R2-filter-werling.sh │ │ │ ├── post-impute-03-isec-3.sh │ │ │ ├── post-impute-03-isec-8.sh │ │ │ └── post-impute-03-isec-merge.sh │ │ ├── run.sh │ │ └── snakemake.sh │ ├── pre-imputation │ │ ├── bgzip.sh │ │ ├── hdbr-01.sh │ │ ├── hdbr-02.split.chr.sh │ │ ├── libd-01.sh │ │ ├── libd-02.conform-gt.sh │ │ ├── obrien-01.sh │ │ ├── obrien-02.split.chr.sh │ │ ├── plinkQC.R │ │ ├── werling-01.sh │ │ └── werling-02.split.chr.sh │ └── readme.md ├── 03-rnaseq │ ├── check.ipynb │ ├── fastqc.sh │ ├── index.sh │ ├── picard.sh │ ├── picard_merge_metrics.R │ ├── readme.md │ ├── run_verifybamid.sh │ ├── salmon.sh │ ├── salmon_readme │ └── star.sh ├── 04-QTL │ ├── apex │ │ ├── Snakefile │ │ ├── apex_analysis.ipynb │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── scripts │ │ │ ├── find_unrel.R │ │ │ ├── fix_factor.R │ │ │ ├── gds2bed.R │ │ │ ├── ibd_king.R │ │ │ ├── king_to_matrix.R │ │ │ ├── kinship_plots.R │ │ │ ├── ld_prune.R │ │ │ ├── make_apex_grm.R │ │ │ ├── make_apex_kin_mat.R │ │ │ ├── make_pheno_file_dummy.R │ │ │ ├── merge_gds.R │ │ │ ├── pca_byrel.R │ │ │ ├── pca_plots_by_group.R │ │ │ ├── pcrelate.R │ │ │ ├── pcrelate_beta.R │ │ │ ├── pcrelate_correct.R │ │ │ ├── unique_variant_ids.R │ │ │ └── vcf2gds.R │ │ └── snakemake.sh │ ├── cis-eQTL │ │ ├── Snakefile │ │ ├── all_genes_batch_expr.R │ │ ├── all_genes_batch_expr.sh │ │ ├── ancestry.ipynb │ │ ├── avg.var.tsv │ │ ├── cibersort.ipynb │ │ ├── cish2_cellprop_correlation.ipynb │ │ ├── cluster_jobscript.sh │ │ ├── combat-seq.ipynb │ │ ├── config.yaml │ │ ├── decon.ipynb │ │ ├── decon.sh │ │ ├── decon.smk │ │ ├── eqtl_analysis.ipynb │ │ ├── fetal_adult.ipynb │ │ ├── func_enrich.ipynb │ │ ├── gtex_eqtl_chr.sh │ │ ├── gtex_eqtl_chr_tri.sh │ │ ├── h2_NPC_neuron.ipynb │ │ ├── metadata.ipynb │ │ ├── module_eigengene.ipynb │ │ ├── pLI.ipynb │ │ ├── paintor.ipynb │ │ ├── paintor.sh │ │ ├── paintor.smk │ │ ├── paintor_fixLD.sh │ │ ├── qvalue_pi0.sh │ │ ├── run_paintor.sh │ │ ├── run_paintor_gene.txt │ │ ├── scripts │ │ │ ├── CIBERSORT.R │ │ │ ├── aFC.py │ │ │ ├── aFC_DanielVo.py │ │ │ ├── add_vep.R │ │ │ ├── ancestry_cov.R │ │ │ ├── ancestry_expr.R │ │ │ ├── calculate_sebeta.R │ │ │ ├── call_nominal.R │ │ │ ├── call_perm.R │ │ │ ├── cov.R │ │ │ ├── decon_cov.R │ │ │ ├── expr_prep.R │ │ │ ├── fix_decon_dosage.R │ │ │ ├── make_annot.R │ │ │ ├── make_susie_expr.R │ │ │ ├── make_susie_meta.R │ │ │ ├── nominal_effect_size_scatter_plot.R │ │ │ ├── paintor_annot.R │ │ │ ├── paintor_fixLD.R │ │ │ ├── paintor_ld.R │ │ │ ├── paintor_zscore.R │ │ │ ├── permutations_all_threshold.R │ │ │ ├── qvalue_pi0_e.R │ │ │ ├── qvalue_pi0_iso.R │ │ │ ├── run_susie_customized.R │ │ │ └── scatter_plot.R │ │ ├── sex_specific.ipynb │ │ ├── snakemake.sh │ │ ├── susie.ipynb │ │ ├── tri_aFC.sh │ │ ├── tri_egene_biotype.ipynb │ │ ├── tri_h2_supp.ipynb │ │ ├── tri_specific.ipynb │ │ └── walker_fetal.ipynb │ ├── cis-isoQTL │ │ ├── Snakefile │ │ ├── XRN2_isoform.ipynb │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── gtex_isoqtl_chr.sh │ │ ├── gtex_isoqtl_chr_tri.sh │ │ ├── iso_make_bed_file.R │ │ ├── iso_make_grp_file.R │ │ ├── isoqtl_analysis.ipynb │ │ ├── prep.ipynb │ │ └── snakemake.sh │ ├── cis-sQTL │ │ ├── Snakefile │ │ ├── allBAMfiltered.txt │ │ ├── allBAMprefix.txt │ │ ├── ancestry_fastqtl_perm.sh │ │ ├── check.ipynb │ │ ├── chr_remove.txt │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── e_iso_s.ipynb │ │ ├── gtex_fastqtl.sh │ │ ├── gtex_fastqtl_merge.sh │ │ ├── gtex_sqtl_chr.sh │ │ ├── gtex_sqtl_chr_tri.sh │ │ ├── juncfiles.txt │ │ ├── qvalue_pi0.ipynb │ │ ├── qvalue_pi0_s_s.sh │ │ ├── revision_walker_hdbr │ │ │ ├── hdbr_call_nominal.sh │ │ │ ├── hdbr_call_perm.sh │ │ │ ├── hdbr_fastqtl_nominal.sh │ │ │ ├── hdbr_fastqtl_perm.sh │ │ │ ├── hdbr_samples.txt │ │ │ ├── obrien_samples.txt │ │ │ ├── pair.sh │ │ │ ├── pair1.sh │ │ │ ├── pair2.sh │ │ │ ├── qvalue_pi0_prep.sh │ │ │ ├── revision.ipynb │ │ │ ├── walker_call_nominal.sh │ │ │ ├── walker_call_perm.sh │ │ │ ├── walker_fastqtl_nominal.sh │ │ │ ├── walker_fastqtl_perm.sh │ │ │ └── walker_samples.txt │ │ ├── run_ancestry_fastqtl_perm.sh │ │ ├── scripts │ │ │ ├── ancestry_lc.R │ │ │ ├── annotate_intron.R │ │ │ ├── cov.R │ │ │ ├── gtf2leafcutter_all_exons_ensg.pl │ │ │ ├── make_all_exons.R │ │ │ ├── make_grp_and_bed_file.R │ │ │ ├── map_clusters_to_genes.R │ │ │ ├── pheno_process.R │ │ │ ├── qvalue_pi0_s.R │ │ │ ├── qvalue_pi0_s_s.R │ │ │ ├── summarise_annot.R │ │ │ └── write_chr_blacklist.R │ │ ├── snakemake.sh │ │ ├── sqtl_analysis.ipynb │ │ ├── step-01-qsub.sh │ │ ├── step-01-star-1stpass.sh │ │ ├── step-02-filter.sh │ │ ├── step-03-qsub.sh │ │ ├── step-03-star-2ndpass.sh │ │ ├── step-04-wasp.sh │ │ └── step-05-bam2junc.sh │ ├── readme.md │ └── trans │ │ ├── Snakefile │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── gbat.ipynb │ │ ├── scripts │ │ ├── cal_cor.R │ │ ├── cal_cor_covar.R │ │ ├── cal_goos_fix_chr.R │ │ ├── cal_pearsonR.R │ │ ├── cal_qval.R │ │ ├── cvp.R │ │ ├── featureCounts │ │ ├── func_norm.R │ │ ├── func_plink.R │ │ ├── func_reml.R │ │ ├── get_gen_pos.R │ │ ├── get_pval_trans_perm_interchrom.R │ │ ├── get_rdata.R │ │ ├── gtf_filter.R │ │ ├── make_smartsva.R │ │ ├── make_sva.R │ │ ├── plink │ │ ├── run_sig.sh │ │ ├── summarize_gene_pair.R │ │ ├── summarize_sig_genes_fromP.R │ │ └── sva.R │ │ └── snakemake.sh ├── 05-QTL-GWAS │ ├── MESC │ │ ├── MESC.ipynb │ │ ├── Snakefile │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── scripts │ │ │ ├── expr_rel.R │ │ │ ├── plink_covar.R │ │ │ └── set_file.R │ │ ├── snakemake.sh │ │ ├── test.sh │ │ └── test.smk │ ├── TWAS │ │ ├── FOCUS.ipynb │ │ ├── LDREF.ipynb │ │ ├── Snakefile │ │ ├── TWAS.ipynb │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── isotwas_miamiplot.ipynb │ │ ├── panel.txt │ │ ├── run_focus.sh │ │ ├── scripts │ │ │ ├── FUSION.profile_wgt_custom.R │ │ │ ├── make_pos_file.R │ │ │ └── write_wgtlist.R │ │ └── snakemake.sh │ ├── coloc_ecaviar_May_2024 │ │ ├── ADHD.Demontis.2019_loci.tsv │ │ ├── ALZ.Bellenguez.2022_loci.tsv │ │ ├── ALZ.Jansen.2019_loci.tsv │ │ ├── ASD.iPSYCHPGC.2018_loci.tsv │ │ ├── MDD.Howard.PGC.2019_loci.tsv │ │ ├── PGC3_SCZ_wave3.european.autosome.public.v3_loci.tsv │ │ ├── cluster_jobscript.sh │ │ ├── coloc-susie.ipynb │ │ ├── coloc.sh │ │ ├── coloc.smk │ │ ├── coloc_rosmap_bash.sh │ │ ├── coloc_rosmap_sneqtl.smk │ │ ├── config.yaml │ │ ├── ecaviar.sh │ │ ├── ecaviar.smk │ │ ├── ecaviar_bash.sh │ │ ├── ecaviar_ld_fetal_bash.sh │ │ ├── ecaviar_locus_feature_bash.sh │ │ ├── ecaviar_run.sh │ │ ├── ecaviar_run.smk │ │ ├── ecaviar_sig_bash.sh │ │ ├── locusplot.ipynb │ │ ├── pgc-bip2021-all_loci.tsv │ │ └── scripts │ │ │ ├── analyze.R │ │ │ ├── coloc_MB.R │ │ │ ├── coloc_annot.R │ │ │ ├── coloc_fetal.R │ │ │ ├── coloc_rosmap_sneqtl.R │ │ │ ├── coloc_thistle.R │ │ │ ├── ecaviar_annot_temp.R │ │ │ ├── locus_egene_MB.R │ │ │ ├── locus_feature.R │ │ │ └── locus_probe.R │ ├── colocal │ │ ├── 20230522_Visualizing_Loci_working.ipynb │ │ ├── GRIN2A.ipynb │ │ ├── Manifest.toml │ │ ├── Project.toml │ │ ├── README │ │ ├── SP4_gviz.ipynb │ │ ├── celltype.sh │ │ ├── celltype.smk │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── eCAVIAR.ipynb │ │ ├── eCAVIAR_500kb.ipynb │ │ ├── eqtl.sh │ │ ├── eqtl.smk │ │ ├── iso_s_bash │ │ │ ├── analyze.sh │ │ │ ├── isoqtl_extract_cis_list.txt │ │ │ ├── sqtl_extract_cis.sh │ │ │ ├── sqtl_extract_cis_list.txt │ │ │ ├── zscore_submit.sh │ │ │ └── zscore_submit_ct.sh │ │ ├── isoqtl.sh │ │ ├── isoqtl.smk │ │ ├── locuszoom_working.txt │ │ ├── mod_ieqtl.sh │ │ ├── mod_ieqtl.smk │ │ ├── sashimipy │ │ │ ├── sashimipy.pdf │ │ │ ├── sashimipy.sh │ │ │ ├── sashimipy1.pdf │ │ │ ├── sashimipy_density.tsv │ │ │ └── sashimipy_density1.tsv │ │ ├── scripts │ │ │ ├── analyze.R │ │ │ ├── analyze_ct.R │ │ │ ├── analyze_iso_s.R │ │ │ ├── analyze_mod.R │ │ │ ├── ecaviar.sh │ │ │ ├── extract_cis_assoc.sh │ │ │ ├── ld_1kg.sh │ │ │ ├── ld_isoqtl.sh │ │ │ ├── ld_sqtl.sh │ │ │ ├── ld_tri.sh │ │ │ ├── locus_egene.R │ │ │ ├── locus_egene_ct.R │ │ │ ├── locus_egene_sex_tri.R │ │ │ ├── locus_intron.R │ │ │ ├── locus_intron_sex_tri.R │ │ │ ├── locus_isoform.R │ │ │ ├── locus_isoform_sex_tri.R │ │ │ ├── zscore.R │ │ │ ├── zscore_ct.R │ │ │ ├── zscore_iso_s.R │ │ │ ├── zscore_mod.R │ │ │ └── zscore_sex_tri.R │ │ ├── sex_tri.sh │ │ ├── sex_tri.smk │ │ ├── sqtl.sh │ │ ├── sqtl.smk │ │ ├── sqtl_map_to_genes.txt │ │ ├── sqtlviztools.ipynb │ │ ├── tables │ │ │ ├── ADHD.Demontis.2019_1Mb.txt │ │ │ ├── ASD.iPSYCHPGC.2018_1Mb.txt │ │ │ ├── MDD.Howard.PGC.2019_1Mb.txt │ │ │ ├── PGC3_SCZ_wave3.european.autosome.public.v3_1Mb.txt │ │ │ ├── PGC3_SCZ_wave3.european.autosome.public.v3_1Mb_table.txt │ │ │ ├── PGC3_SCZ_wave3_public.v2_1Mb.txt │ │ │ ├── SCZ.Clozuk.2018_1Mb.txt │ │ │ └── pgc-bip2021-all_1Mb.txt │ │ └── temp.ipynb │ ├── readme.md │ └── sLDSC │ │ ├── Snakefile │ │ ├── cluster_jobscript.sh │ │ ├── config.yaml │ │ ├── ldsc_analysis.ipynb │ │ ├── pec.sh │ │ ├── pec.smk │ │ ├── qqplot.sh │ │ ├── scripts │ │ ├── make_annot_customed.py │ │ ├── make_annot_maxcpp.R │ │ ├── qqplot.R │ │ ├── set_file.R │ │ ├── set_file_grp_perm.R │ │ ├── set_file_isoqtl.R │ │ ├── set_file_sqtl.R │ │ ├── set_file_susie.R │ │ └── variant_coord.R │ │ └── snakemake.sh └── 06-analyses │ ├── 01-egene-sgene-enrichment │ ├── fetal_only_egenes.ipynb │ └── trimester_egenes_sgenes.ipynb │ ├── 02-wgcna │ ├── compare_module_enrichment.ipynb │ ├── dashboard_generator.ipynb │ └── dashboards │ │ ├── M001-tr2.pdf │ │ ├── M002-gene.pdf │ │ ├── M003-xx.pdf │ │ ├── M004-xy.pdf │ │ ├── M005-iso.pdf │ │ ├── M006-iso.pdf │ │ ├── M007-tr1.pdf │ │ ├── M008-xy.pdf │ │ ├── M009-iso.pdf │ │ ├── M010-iso.pdf │ │ ├── M011-iso.pdf │ │ ├── M012-gene.pdf │ │ ├── M013-xy.pdf │ │ ├── M014-xx.pdf │ │ ├── M015-gene.pdf │ │ ├── M016-xy.pdf │ │ ├── M017-tr1.pdf │ │ ├── M018-xx.pdf │ │ ├── M019-gene.pdf │ │ ├── M020-tr2.pdf │ │ ├── M021-xy.pdf │ │ ├── M022-iso.pdf │ │ ├── M023-tr1.pdf │ │ ├── M024-gene.pdf │ │ ├── M025-tr2.pdf │ │ ├── M026-xx.pdf │ │ ├── M027-tr1.pdf │ │ ├── M028-tr1.pdf │ │ ├── M029-iso.pdf │ │ ├── M030-gene.pdf │ │ ├── M031-iso.pdf │ │ ├── M032-tr1.pdf │ │ ├── M033-tr1.pdf │ │ ├── M034-tr2.pdf │ │ ├── M035-iso.pdf │ │ ├── M036-xy.pdf │ │ ├── M037-gene.pdf │ │ ├── M038-xx.pdf │ │ ├── M039-tr1.pdf │ │ ├── M040-iso.pdf │ │ ├── M041-tr1.pdf │ │ ├── M042-xx.pdf │ │ ├── M043-iso.pdf │ │ ├── M044-tr1.pdf │ │ ├── M045-iso.pdf │ │ ├── M046-tr2.pdf │ │ ├── M047-xy.pdf │ │ ├── M048-tr1.pdf │ │ ├── M049-gene.pdf │ │ ├── M050-xx.pdf │ │ ├── M051-iso.pdf │ │ ├── M052-tr2.pdf │ │ ├── M053-xy.pdf │ │ ├── M054-iso.pdf │ │ ├── M055-gene.pdf │ │ ├── M056-xx.pdf │ │ ├── M057-xx.pdf │ │ ├── M058-gene.pdf │ │ ├── M059-iso.pdf │ │ ├── M060-tr2.pdf │ │ ├── M061-tr1.pdf │ │ ├── M062-xy.pdf │ │ ├── M063-gene.pdf │ │ ├── M064-xx.pdf │ │ ├── M065-iso.pdf │ │ ├── M066-gene.pdf │ │ ├── M067-xx.pdf │ │ ├── M068-iso.pdf │ │ ├── M069-gene.pdf │ │ ├── M070-tr1.pdf │ │ ├── M071-xy.pdf │ │ ├── M072-tr2.pdf │ │ ├── M073-xx.pdf │ │ ├── M074-tr1.pdf │ │ ├── M075-iso.pdf │ │ ├── M076-iso.pdf │ │ ├── M077-iso.pdf │ │ ├── M078-gene.pdf │ │ ├── M079-xx.pdf │ │ ├── M080-tr2.pdf │ │ ├── M081-xy.pdf │ │ ├── M082-iso.pdf │ │ ├── M083-tr2.pdf │ │ ├── M084-gene.pdf │ │ ├── M085-xx.pdf │ │ ├── M086-gene.pdf │ │ ├── M087-tr2.pdf │ │ ├── M088-xx.pdf │ │ ├── M089-iso.pdf │ │ ├── M090-tr1.pdf │ │ ├── M091-xy.pdf │ │ ├── M092-iso.pdf │ │ ├── M093-tr1.pdf │ │ ├── M094-xy.pdf │ │ ├── M095-xy.pdf │ │ ├── M096-tr1.pdf │ │ ├── M097-gene.pdf │ │ ├── M098-xx.pdf │ │ ├── M099-iso.pdf │ │ ├── M100-xx.pdf │ │ ├── M101-xy.pdf │ │ ├── M102-gene.pdf │ │ ├── M103-tr1.pdf │ │ ├── M104-tr2.pdf │ │ ├── M105-iso.pdf │ │ ├── M106-tr2.pdf │ │ ├── M107-tr1.pdf │ │ ├── M108-xx.pdf │ │ ├── M109-gene.pdf │ │ ├── M110-xy.pdf │ │ ├── M111-tr1.pdf │ │ ├── M112-xx.pdf │ │ ├── M113-xy.pdf │ │ ├── M114-gene.pdf │ │ ├── M115-tr2.pdf │ │ ├── M116-tr1.pdf │ │ ├── M117-iso.pdf │ │ ├── M118-tr2.pdf │ │ ├── M119-xy.pdf │ │ ├── M120-iso.pdf │ │ ├── M121-tr1.pdf │ │ ├── M122-iso.pdf │ │ ├── M123-iso.pdf │ │ └── M124-iso.pdf │ └── README.md └── data └── accessory_files ├── gencode.v33lift37.annotation.gene.info.tsv └── rare_variant_list.rds /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gandallab/devBrain_xQTL/HEAD/README.md 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