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 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.mergedReg2Map.EUR.5 \
--bfile /tmp/ldsc-2024-06-24-FdppcmJSsY/1000G.EUR.HM3.5 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.5.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 14:11:57 2024
Read list of 75743 SNPs from /tmp/ldsc-2024-06-24-FdppcmJSsY/1000G.EUR.HM3.5.bim
Read 1 annotations for 75743 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.5.annot.gz
Read list of 503 individuals from /tmp/ldsc-2024-06-24-FdppcmJSsY/1000G.EUR.HM3.5.fam
Reading genotypes from /tmp/ldsc-2024-06-24-FdppcmJSsY/1000G.EUR.HM3.5.bed
After filtering, 75743 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 75743 SNPs will be printed.
Writing LD Scores for 75743 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.5.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.5.l2.ldscore.gz
         MAF       L2
mean  0.2355   3.0230
std   0.1429   3.4183
min   0.0020  -0.1536
25%   0.1103   0.8943
50%   0.2266   2.0265
75%   0.3559   3.9278
max   0.5000  34.8396

MAF/LD Score Correlation Matrix
     MAF   L2
MAF  1.0  0.2
L2   0.2  1.0

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    11443

Summary of Annotation Matrix Row Sums
count    75743.0000
mean         0.1511
std          0.3581
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 14:14:24 2024
Total time elapsed: 2.0m:27.04s
Done.