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.5 \
--bfile /tmp/ldsc-2024-06-24-CBN412XUie/1000G.AFR.HM3.5 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.5.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:32 2024
Read list of 75284 SNPs from /tmp/ldsc-2024-06-24-CBN412XUie/1000G.AFR.HM3.5.bim
Read 1 annotations for 75284 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.5.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-CBN412XUie/1000G.AFR.HM3.5.fam
Reading genotypes from /tmp/ldsc-2024-06-24-CBN412XUie/1000G.AFR.HM3.5.bed
After filtering, 75284 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 75284 SNPs will be printed.
Writing LD Scores for 75284 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.5.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.5.l2.ldscore.gz
         MAF      L2
mean  0.2284  0.2395
std   0.1463  0.4624
min   0.0015 -0.0377
25%   0.1014  0.0167
50%   0.2186  0.0661
75%   0.3525  0.2282
max   0.5000  7.2119

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.071
L2   0.071  1.000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    1582

Summary of Annotation Matrix Row Sums
count    75284.0000
mean         0.0210
std          0.1434
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:08:42 2024
Total time elapsed: 5.0m:9.92s
Done.