Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.Astro.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.Astro.hg38.AFR.18 \
--bfile /tmp/ldsc-2024-06-24-0WZ4jOzCeD/1000G.AFR.HM3.18 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.AFR.18.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:42 2024
Read list of 35672 SNPs from /tmp/ldsc-2024-06-24-0WZ4jOzCeD/1000G.AFR.HM3.18.bim
Read 1 annotations for 35672 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.AFR.18.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-0WZ4jOzCeD/1000G.AFR.HM3.18.fam
Reading genotypes from /tmp/ldsc-2024-06-24-0WZ4jOzCeD/1000G.AFR.HM3.18.bed
After filtering, 35672 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 35672 SNPs will be printed.
Writing LD Scores for 35672 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.AFR.18.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.AFR.18.l2.ldscore.gz
         MAF      L2
mean  0.2309  0.2550
std   0.1446  0.4998
min   0.0015 -0.0422
25%   0.1067  0.0150
50%   0.2209  0.0690
75%   0.3517  0.2435
max   0.5000  6.3739

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0498
L2   0.0498  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    1018

Summary of Annotation Matrix Row Sums
count    35672.0000
mean         0.0285
std          0.1665
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:05:48 2024
Total time elapsed: 2.0m:5.69s
Done.