.gitignore

.Rproj.user
.Rhistory
.RData
.Ruserdata
core.*
.DS_Store
/**/*.DS_Store
/**/**/*.DS_Store
/*.gz.tbi

# Data files
/Data/GWAS/**/*.txt.gz
/Data/GWAS/**/*.tsv.gz
/Data/QTL/**/**/*.txt.gz 
/Data/GWAS/Nalls23andMe_2019/nallsEtAl2019_allSamples_allVariants.mod.txt
/Data/**/**/_genome_wide/COJO/cojo-file.ma  
/Data/GWAS/**/*.tbi
/Data/GWAS/Kunkle_2019/Kunkle_etal_Stage1_results.tsv 
/Data/GWAS/Kunkle_2019/Kunkle_etal_Stage1_results.tsv.gz 
/Data/GWAS/Kunkle_2019/Kunkle_etal_Stage1_results.tsv.gz.tbi 

# Reference files
/Data/**/**/plink
/Data/Reference/**/**/*.vcf
/Data/Reference/**/**/*.vcf.gz
/Data/Reference/**/**/*.vcf.gz.tbi
/Manuscripts/
/Data/**/**/**/FINEMAP/data.ld
/Data/**/**/**/plink/LD_matrix.RData
/Data/**/**/**/plink/*.RDS
/Data/Reference/UKB_MAF

# Annotations
/echolocatoR/tools/Annotations/*.rds
/echolocatoR/tools/Annotations/psychENCODE/DER-08a_hg19_eQTL.significant.txt
/echolocatoR/tools/Annotations/psychENCODE/DER-10a_hg19_isoQTL.significant.txt
/echolocatoR/tools/Annotations/psychENCODE/*.txt.gz
/echolocatoR/tools/Annotations/ROADMAP/Chromatin_Marks/

# Genome-wide analyses
/Data/**/**/_genome_wide/fGWAS/Input/annotations.Nalls23andMe_2019.txt
## PolyFun specifically 
/Data/**/**/_genome_wide/PolyFun/*.parquet
/Data/**/**/*.parquet
/Data/**/**/_genome_wide/eQTL_catalogue/*.query.tsv.gz 
/Data/GWAS/Nalls23andMe_2019/_genome_wide/IMPACT/annot_melt_topAnnot_all.csv.gz