Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.D1.D2H.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.D2H.hg38.AFR.17 \
--bfile /tmp/ldsc-2024-06-24-qlmg5ePca9/1000G.AFR.HM3.17 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.17.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:32 2024
Read list of 32267 SNPs from /tmp/ldsc-2024-06-24-qlmg5ePca9/1000G.AFR.HM3.17.bim
Read 1 annotations for 32267 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.17.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-qlmg5ePca9/1000G.AFR.HM3.17.fam
Reading genotypes from /tmp/ldsc-2024-06-24-qlmg5ePca9/1000G.AFR.HM3.17.bed
After filtering, 32267 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 32267 SNPs will be printed.
Writing LD Scores for 32267 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.17.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.17.l2.ldscore.gz
         MAF      L2
mean  0.2280  0.2156
std   0.1463  0.4364
min   0.0015 -0.0351
25%   0.1006  0.0087
50%   0.2186  0.0432
75%   0.3517  0.1814
max   0.5000  4.5930

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0631
L2   0.0631  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    645

Summary of Annotation Matrix Row Sums
count    32267.00
mean         0.02
std          0.14
min          0.00
25%          0.00
50%          0.00
75%          0.00
max          1.00
Analysis finished at Mon Jun 24 13:05:47 2024
Total time elapsed: 2.0m:14.28s
Done.