Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.INT.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.INT.hg38.AFR.4 \
--bfile /tmp/ldsc-2024-06-24-e9CetqYnUL/1000G.AFR.HM3.4 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.AFR.4.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:06:58 2024
Read list of 75316 SNPs from /tmp/ldsc-2024-06-24-e9CetqYnUL/1000G.AFR.HM3.4.bim
Read 1 annotations for 75316 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.AFR.4.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-e9CetqYnUL/1000G.AFR.HM3.4.fam
Reading genotypes from /tmp/ldsc-2024-06-24-e9CetqYnUL/1000G.AFR.HM3.4.bed
After filtering, 75316 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 75316 SNPs will be printed.
Writing LD Scores for 75316 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.AFR.4.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.AFR.4.l2.ldscore.gz
         MAF      L2
mean  0.2302  0.2873
std   0.1448  0.5175
min   0.0015 -0.0688
25%   0.1051  0.0222
50%   0.2194  0.0874
75%   0.3525  0.2912
max   0.5000  6.4946

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0856
L2   0.0856  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    2048

Summary of Annotation Matrix Row Sums
count    75316.0000
mean         0.0272
std          0.1626
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:10:43 2024
Total time elapsed: 3.0m:44.73s
Done.