Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.mergedReg2Map 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.mergedReg2Map.AFR.17 \
--bfile /tmp/ldsc-2024-06-24-G9ZeMruk34/1000G.AFR.HM3.17 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.17.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 14:11:57 2024
Read list of 32267 SNPs from /tmp/ldsc-2024-06-24-G9ZeMruk34/1000G.AFR.HM3.17.bim
Read 1 annotations for 32267 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.17.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-G9ZeMruk34/1000G.AFR.HM3.17.fam
Reading genotypes from /tmp/ldsc-2024-06-24-G9ZeMruk34/1000G.AFR.HM3.17.bed
After filtering, 32267 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 32267 SNPs will be printed.
Writing LD Scores for 32267 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.17.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.AFR.17.l2.ldscore.gz
         MAF       L2
mean  0.2280   1.7350
std   0.1463   2.0865
min   0.0015  -0.1243
25%   0.1006   0.3873
50%   0.2186   1.0693
75%   0.3517   2.2489
max   0.5000  16.8488

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0826
L2   0.0826  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    5589

Summary of Annotation Matrix Row Sums
count    32267.0000
mean         0.1732
std          0.3784
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 14:13:09 2024
Total time elapsed: 1.0m:12.17s
Done.