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.9 \
--bfile /tmp/ldsc-2024-06-24-qdmdR5emuZ/1000G.EUR.HM3.9 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.9.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:08:09 2024
Read list of 55879 SNPs from /tmp/ldsc-2024-06-24-qdmdR5emuZ/1000G.EUR.HM3.9.bim
Read 1 annotations for 55879 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.9.annot.gz
Read list of 503 individuals from /tmp/ldsc-2024-06-24-qdmdR5emuZ/1000G.EUR.HM3.9.fam
Reading genotypes from /tmp/ldsc-2024-06-24-qdmdR5emuZ/1000G.EUR.HM3.9.bed
After filtering, 55879 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 55879 SNPs will be printed.
Writing LD Scores for 55879 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.9.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.9.l2.ldscore.gz
         MAF       L2
mean  0.2342   0.4519
std   0.1431   0.9037
min   0.0020  -0.0791
25%   0.1093   0.0112
50%   0.2227   0.0823
75%   0.3549   0.4759
max   0.5000  10.8159

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.132
L2   0.132  1.000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    1283

Summary of Annotation Matrix Row Sums
count    55879.0000
mean         0.0230
std          0.1498
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:09:53 2024
Total time elapsed: 1.0m:43.48s
Done.