Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.OPC.hg38 bed regions
making annot file
Computing partitioned LD scores for hg38 for EUR.
*********************************************************************
* 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.OPC.hg38.EUR.16 \
--bfile /tmp/ldsc-2024-06-24-S7mMpqI9r4/1000G.EUR.HM3.16 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.16.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:09:50 2024
Read list of 36853 SNPs from /tmp/ldsc-2024-06-24-S7mMpqI9r4/1000G.EUR.HM3.16.bim
Read 1 annotations for 36853 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.16.annot.gz
Read list of 503 individuals from /tmp/ldsc-2024-06-24-S7mMpqI9r4/1000G.EUR.HM3.16.fam
Reading genotypes from /tmp/ldsc-2024-06-24-S7mMpqI9r4/1000G.EUR.HM3.16.bed
After filtering, 36853 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 36853 SNPs will be printed.
Writing LD Scores for 36853 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.16.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.16.l2.ldscore.gz
         MAF      L2
mean  0.2371  0.6047
std   0.1434  1.0986
min   0.0020 -0.0740
25%   0.1113  0.0298
50%   0.2286  0.1597
75%   0.3588  0.7267
max   0.5000  9.6243

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.049
L2   0.049  1.000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    1192

Summary of Annotation Matrix Row Sums
count    36853.0000
mean         0.0323
std          0.1769
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:11:39 2024
Total time elapsed: 1.0m:48.46s
Done.