Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.D2.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.D2.Matrix.hg38.AFR.6 \
--bfile /tmp/ldsc-2024-06-24-yRe3o84T7v/1000G.AFR.HM3.6 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.AFR.6.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:05:19 2024
Read list of 73528 SNPs from /tmp/ldsc-2024-06-24-yRe3o84T7v/1000G.AFR.HM3.6.bim
Read 1 annotations for 73528 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.AFR.6.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-yRe3o84T7v/1000G.AFR.HM3.6.fam
Reading genotypes from /tmp/ldsc-2024-06-24-yRe3o84T7v/1000G.AFR.HM3.6.bed
After filtering, 73528 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 73528 SNPs will be printed.
Writing LD Scores for 73528 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.AFR.6.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.AFR.6.l2.ldscore.gz
         MAF      L2
mean  0.2216  0.5822
std   0.1455  0.8482
min   0.0015 -0.0776
25%   0.0953  0.0823
50%   0.2095  0.2463
75%   0.3419  0.7270
max   0.5000  9.0914

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1035
L2   0.1035  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    3821

Summary of Annotation Matrix Row Sums
count    73528.000
mean         0.052
std          0.222
min          0.000
25%          0.000
50%          0.000
75%          0.000
max          1.000
Analysis finished at Mon Jun 24 13:09:44 2024
Total time elapsed: 4.0m:24.66s
Done.