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* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
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Call: 
./ldsc.py \
--h2-cts /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/Glaucoma-Choquet_2018.sumstats.gz \
--ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR. \
--out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/enrichments/Human_Striatum_snATAC.Glaucoma-Choquet_2018.EUR \
--ref-ld-chr-cts /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/Human_Striatum_snATAC.EUR_hg38.ldcts \
--w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. 

Beginning analysis at Sat Jun 22 15:08:31 2024
Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/Glaucoma-Choquet_2018.sumstats.gz ...
Read summary statistics for 1195704 SNPs.
Reading reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR.[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1198864 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC.[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1198864 SNPs.
After merging with reference panel LD, 1183089 SNPs remain.
After merging with regression SNP LD, 1183089 SNPs remain.
Removed 54 SNPs with chi^2 > 80 (1183035 SNPs remain)
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.EUR.[1-22] ... (ldscore_fromlist)
Performing regression.
Results printed to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/enrichments/Human_Striatum_snATAC.Glaucoma-Choquet_2018.EUR.cell_type_results.txt
Analysis finished at Sat Jun 22 15:21:07 2024
Total time elapsed: 12.0m:36.05s