Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.OPC.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.OPC.hg38.AFR.2 \
--bfile /tmp/ldsc-2024-06-24-N9nN1TXU2C/1000G.AFR.HM3.2 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.2.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:09:14 2024
Read list of 100252 SNPs from /tmp/ldsc-2024-06-24-N9nN1TXU2C/1000G.AFR.HM3.2.bim
Read 1 annotations for 100252 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.2.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-N9nN1TXU2C/1000G.AFR.HM3.2.fam
Reading genotypes from /tmp/ldsc-2024-06-24-N9nN1TXU2C/1000G.AFR.HM3.2.bed
After filtering, 100252 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 100252 SNPs will be printed.
Writing LD Scores for 100252 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.2.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.2.l2.ldscore.gz
         MAF       L2
mean  0.2298   0.3293
std   0.1451   0.6037
min   0.0015  -0.0439
25%   0.1044   0.0316
50%   0.2209   0.1072
75%   0.3525   0.3500
max   0.5000  14.0939

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0518
L2   0.0518  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    2949

Summary of Annotation Matrix Row Sums
count    100252.0000
mean          0.0294
std           0.1690
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Mon Jun 24 13:12:45 2024
Total time elapsed: 3.0m:30.84s
Done.