Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.mergedReg2Map 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.mergedReg2Map.AFR.21 \
--bfile /tmp/ldsc-2024-06-24-vmkRPx7Ocm/1000G.AFR.HM3.21 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.21.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 14:11:57 2024
Read list of 17085 SNPs from /tmp/ldsc-2024-06-24-vmkRPx7Ocm/1000G.AFR.HM3.21.bim
Read 1 annotations for 17085 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.21.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-vmkRPx7Ocm/1000G.AFR.HM3.21.fam
Reading genotypes from /tmp/ldsc-2024-06-24-vmkRPx7Ocm/1000G.AFR.HM3.21.bed
After filtering, 17085 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 17085 SNPs will be printed.
Writing LD Scores for 17085 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.21.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.21.l2.ldscore.gz
         MAF       L2
mean  0.2291   1.3192
std   0.1449   1.5299
min   0.0015  -0.0823
25%   0.1036   0.3091
50%   0.2194   0.7854
75%   0.3510   1.7651
max   0.5000  11.8944

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0974
L2   0.0974  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    2509

Summary of Annotation Matrix Row Sums
count    17085.0000
mean         0.1469
std          0.3540
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 14:12:37 2024
Total time elapsed: 39.85s
Done.