Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.D1.Matrix.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.D1.Matrix.hg38.EUR.2 \
--bfile /tmp/ldsc-2024-06-24-0kwxyw9nHv/1000G.EUR.HM3.2 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.2.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:48 2024
Read list of 100669 SNPs from /tmp/ldsc-2024-06-24-0kwxyw9nHv/1000G.EUR.HM3.2.bim
Read 1 annotations for 100669 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.2.annot.gz
Read list of 503 individuals from /tmp/ldsc-2024-06-24-0kwxyw9nHv/1000G.EUR.HM3.2.fam
Reading genotypes from /tmp/ldsc-2024-06-24-0kwxyw9nHv/1000G.EUR.HM3.2.bed
After filtering, 100669 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 100669 SNPs will be printed.
Writing LD Scores for 100669 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.2.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.2.l2.ldscore.gz
         MAF       L2
mean  0.2367   1.1376
std   0.1439   1.6882
min   0.0020  -0.1065
25%   0.1103   0.1299
50%   0.2276   0.5048
75%   0.3598   1.4510
max   0.5000  16.2842

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1582
L2   0.1582  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    5045

Summary of Annotation Matrix Row Sums
count    100669.0000
mean          0.0501
std           0.2182
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Mon Jun 24 13:09:03 2024
Total time elapsed: 5.0m:14.59s
Done.