Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.D1.Matrix.hg38 bed regions
making annot file
Computing partitioned LD scores for hg38 for AFR.
*********************************************************************
* 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
*********************************************************************
Call: 
./ldsc.py \
--print-snps /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_EUR_Phase3_GRCh38_files/hapmap3_snps/listHM3.noMHC.txt \
--out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.5 \
--bfile /tmp/ldsc-2024-06-24-D16G4dCwhr/1000G.AFR.HM3.5 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.5.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:49 2024
Read list of 75284 SNPs from /tmp/ldsc-2024-06-24-D16G4dCwhr/1000G.AFR.HM3.5.bim
Read 1 annotations for 75284 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.5.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-D16G4dCwhr/1000G.AFR.HM3.5.fam
Reading genotypes from /tmp/ldsc-2024-06-24-D16G4dCwhr/1000G.AFR.HM3.5.bed
After filtering, 75284 SNPs remain
Estimating LD Score.
Reading list of 1215001 SNPs for which to print LD Scores from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_EUR_Phase3_GRCh38_files/hapmap3_snps/listHM3.noMHC.txt
After merging with --print-snps, LD Scores for 75284 SNPs will be printed.
Writing LD Scores for 75284 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.5.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.5.l2.ldscore.gz
         MAF      L2
mean  0.2284  0.5520
std   0.1463  0.7933
min   0.0015 -0.0538
25%   0.1014  0.0840
50%   0.2186  0.2441
75%   0.3525  0.7047
max   0.5000  8.0743

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1011
L2   0.1011  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    3838

Summary of Annotation Matrix Row Sums
count    75284.000
mean         0.051
std          0.220
min          0.000
25%          0.000
50%          0.000
75%          0.000
max          1.000
Analysis finished at Mon Jun 24 13:08:21 2024
Total time elapsed: 4.0m:32.39s
Done.