Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.OPC.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.OPC.hg38.AFR.22 \
--bfile /tmp/ldsc-2024-06-24-psK5bC4DPx/1000G.AFR.HM3.22 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.22.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:09:32 2024
Read list of 17585 SNPs from /tmp/ldsc-2024-06-24-psK5bC4DPx/1000G.AFR.HM3.22.bim
Read 1 annotations for 17585 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.22.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-psK5bC4DPx/1000G.AFR.HM3.22.fam
Reading genotypes from /tmp/ldsc-2024-06-24-psK5bC4DPx/1000G.AFR.HM3.22.bed
After filtering, 17585 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 17585 SNPs will be printed.
Writing LD Scores for 17585 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.22.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.22.l2.ldscore.gz
         MAF      L2
mean  0.2165  0.3539
std   0.1478  0.5468
min   0.0015 -0.0457
25%   0.0855  0.0363
50%   0.2012  0.1338
75%   0.3404  0.4211
max   0.5000  5.6283

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000 -0.011
L2  -0.011  1.000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    608

Summary of Annotation Matrix Row Sums
count    17585.0000
mean         0.0346
std          0.1827
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:10:13 2024
Total time elapsed: 40.93s
Done.