Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.Microglia.hg38 bed regions
making annot file
Computing partitioned LD scores for hg38 for EUR.
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* 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.Microglia.hg38.EUR.10 \
--bfile /tmp/ldsc-2024-06-24-qSK3E5gl6L/1000G.EUR.HM3.10 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.10.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:08:11 2024
Read list of 64659 SNPs from /tmp/ldsc-2024-06-24-qSK3E5gl6L/1000G.EUR.HM3.10.bim
Read 1 annotations for 64659 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.10.annot.gz
Read list of 503 individuals from /tmp/ldsc-2024-06-24-qSK3E5gl6L/1000G.EUR.HM3.10.fam
Reading genotypes from /tmp/ldsc-2024-06-24-qSK3E5gl6L/1000G.EUR.HM3.10.bed
After filtering, 64659 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 64659 SNPs will be printed.
Writing LD Scores for 64659 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.10.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.10.l2.ldscore.gz
         MAF      L2
mean  0.2309  0.4885
std   0.1435  0.8832
min   0.0020 -0.0855
25%   0.1054  0.0134
50%   0.2177  0.0956
75%   0.3529  0.5797
max   0.5000  9.5823

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1095
L2   0.1095  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    1688

Summary of Annotation Matrix Row Sums
count    64659.0000
mean         0.0261
std          0.1595
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:11:32 2024
Total time elapsed: 3.0m:21.02s
Done.