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.19 \
--bfile /tmp/ldsc-2024-06-24-GSdx8lDHe3/1000G.EUR.HM3.19 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.19.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 14:11:57 2024
Read list of 22710 SNPs from /tmp/ldsc-2024-06-24-GSdx8lDHe3/1000G.EUR.HM3.19.bim
Read 1 annotations for 22710 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.19.annot.gz
Read list of 503 individuals from /tmp/ldsc-2024-06-24-GSdx8lDHe3/1000G.EUR.HM3.19.fam
Reading genotypes from /tmp/ldsc-2024-06-24-GSdx8lDHe3/1000G.EUR.HM3.19.bed
After filtering, 22710 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 22710 SNPs will be printed.
Writing LD Scores for 22710 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.19.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.19.l2.ldscore.gz
         MAF       L2
mean  0.2363   2.3348
std   0.1431   2.4171
min   0.0020  -0.1656
25%   0.1113   0.5854
50%   0.2311   1.5862
75%   0.3559   3.2672
max   0.5000  17.8956

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1749
L2   0.1749  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    3991

Summary of Annotation Matrix Row Sums
count    22710.0000
mean         0.1757
std          0.3806
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 14:15:24 2024
Total time elapsed: 3.0m:26.68s
Done.