Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.D2.Striosome.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.Striosome.hg38.AFR.6 \
--bfile /tmp/ldsc-2024-06-24-PnR3EnykCF/1000G.AFR.HM3.6 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.6.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:06:20 2024
Read list of 73528 SNPs from /tmp/ldsc-2024-06-24-PnR3EnykCF/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.Striosome.hg38.AFR.6.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-PnR3EnykCF/1000G.AFR.HM3.6.fam
Reading genotypes from /tmp/ldsc-2024-06-24-PnR3EnykCF/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.Striosome.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.Striosome.hg38.AFR.6.l2.ldscore.gz
         MAF      L2
mean  0.2216  0.4268
std   0.1455  0.6490
min   0.0015 -0.0796
25%   0.0953  0.0535
50%   0.2095  0.1667
75%   0.3419  0.5077
max   0.5000  8.1942

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1064
L2   0.1064  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    2885

Summary of Annotation Matrix Row Sums
count    73528.0000
mean         0.0392
std          0.1942
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:11:51 2024
Total time elapsed: 5.0m:31.0s
Done.