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.2 \
--bfile /tmp/ldsc-2024-06-24-AfZj0eYtd0/1000G.AFR.HM3.2 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.2.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:49 2024
Read list of 100252 SNPs from /tmp/ldsc-2024-06-24-AfZj0eYtd0/1000G.AFR.HM3.2.bim
Read 1 annotations for 100252 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.2.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-AfZj0eYtd0/1000G.AFR.HM3.2.fam
Reading genotypes from /tmp/ldsc-2024-06-24-AfZj0eYtd0/1000G.AFR.HM3.2.bed
After filtering, 100252 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 100252 SNPs will be printed.
Writing LD Scores for 100252 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.2.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.2.l2.ldscore.gz
         MAF       L2
mean  0.2298   0.6110
std   0.1451   0.9201
min   0.0015  -0.0603
25%   0.1044   0.0895
50%   0.2209   0.2556
75%   0.3525   0.7547
max   0.5000  10.4806

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.088
L2   0.088  1.000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    5015

Summary of Annotation Matrix Row Sums
count    100252.000
mean          0.050
std           0.218
min           0.000
25%           0.000
50%           0.000
75%           0.000
max           1.000
Analysis finished at Mon Jun 24 13:09:46 2024
Total time elapsed: 5.0m:57.73s
Done.