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 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.D1.Matrix.hg38.AFR.15 \
--bfile /tmp/ldsc-2024-06-24-zREOcmszHQ/1000G.AFR.HM3.15 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.15.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:48 2024
Read list of 35905 SNPs from /tmp/ldsc-2024-06-24-zREOcmszHQ/1000G.AFR.HM3.15.bim
Read 1 annotations for 35905 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.15.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-zREOcmszHQ/1000G.AFR.HM3.15.fam
Reading genotypes from /tmp/ldsc-2024-06-24-zREOcmszHQ/1000G.AFR.HM3.15.bed
After filtering, 35905 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 35905 SNPs will be printed.
Writing LD Scores for 35905 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.15.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.AFR.15.l2.ldscore.gz
         MAF      L2
mean  0.2309  0.6112
std   0.1469  0.9365
min   0.0015 -0.0468
25%   0.1021  0.0722
50%   0.2209  0.2343
75%   0.3563  0.7659
max   0.5000  8.4142

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0624
L2   0.0624  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    1939

Summary of Annotation Matrix Row Sums
count    35905.000
mean         0.054
std          0.226
min          0.000
25%          0.000
50%          0.000
75%          0.000
max          1.000
Analysis finished at Mon Jun 24 13:06:00 2024
Total time elapsed: 2.0m:11.84s
Done.