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.3 \
--bfile /tmp/ldsc-2024-06-24-tmpz5fLG1f/1000G.AFR.HM3.3 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.3.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:49 2024
Read list of 83630 SNPs from /tmp/ldsc-2024-06-24-tmpz5fLG1f/1000G.AFR.HM3.3.bim
Read 1 annotations for 83630 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.3.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-tmpz5fLG1f/1000G.AFR.HM3.3.fam
Reading genotypes from /tmp/ldsc-2024-06-24-tmpz5fLG1f/1000G.AFR.HM3.3.bed
After filtering, 83630 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 83630 SNPs will be printed.
Writing LD Scores for 83630 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.3.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.3.l2.ldscore.gz
         MAF       L2
mean  0.2302   0.6394
std   0.1468   1.0328
min   0.0015  -0.0640
25%   0.1029   0.0919
50%   0.2201   0.2648
75%   0.3555   0.7732
max   0.5000  13.5232

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.132
L2   0.132  1.000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    4415

Summary of Annotation Matrix Row Sums
count    83630.0000
mean         0.0528
std          0.2236
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:08:49 2024
Total time elapsed: 5.0m:0.4s
Done.