Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.D1.Striosome.hg38 bed regions
making annot file
Computing partitioned LD scores for hg38 for EUR.
*********************************************************************
* 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.Striosome.hg38.EUR.5 \
--bfile /tmp/ldsc-2024-06-24-foBF1icawW/1000G.EUR.HM3.5 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.5.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:03:42 2024
Read list of 75743 SNPs from /tmp/ldsc-2024-06-24-foBF1icawW/1000G.EUR.HM3.5.bim
Read 1 annotations for 75743 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.5.annot.gz
Read list of 503 individuals from /tmp/ldsc-2024-06-24-foBF1icawW/1000G.EUR.HM3.5.fam
Reading genotypes from /tmp/ldsc-2024-06-24-foBF1icawW/1000G.EUR.HM3.5.bed
After filtering, 75743 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 75743 SNPs will be printed.
Writing LD Scores for 75743 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.5.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.5.l2.ldscore.gz
         MAF       L2
mean  0.2355   0.7734
std   0.1429   1.1185
min   0.0020  -0.1012
25%   0.1103   0.0796
50%   0.2266   0.3218
75%   0.3559   1.0413
max   0.5000  11.3307

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1596
L2   0.1596  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    2975

Summary of Annotation Matrix Row Sums
count    75743.0000
mean         0.0393
std          0.1943
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:11:21 2024
Total time elapsed: 7.0m:39.4s
Done.