Partitioning with 1000G LD scores on HapMap3 SNPs with Human_Striatum_snATAC.D2.Striosome.hg38 bed regions
making annot file
Computing partitioned LD scores for hg38 for AFR.
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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.D2.Striosome.hg38.AFR.3 \
--bfile /tmp/ldsc-2024-06-24-wj5NovwhmK/1000G.AFR.HM3.3 \
--thin-annot  \
--annot /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.3.annot.gz \
--l2  \
--ld-wind-kb 1000.0 

Beginning analysis at Mon Jun 24 13:06:09 2024
Read list of 83630 SNPs from /tmp/ldsc-2024-06-24-wj5NovwhmK/1000G.AFR.HM3.3.bim
Read 1 annotations for 83630 SNPs from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.3.annot.gz
Read list of 661 individuals from /tmp/ldsc-2024-06-24-wj5NovwhmK/1000G.AFR.HM3.3.fam
Reading genotypes from /tmp/ldsc-2024-06-24-wj5NovwhmK/1000G.AFR.HM3.3.bed
After filtering, 83630 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 83630 SNPs will be printed.
Writing LD Scores for 83630 SNPs to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.3.l2.ldscore.gz

Summary of LD Scores in /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.3.l2.ldscore.gz
         MAF       L2
mean  0.2302   0.4397
std   0.1468   0.7564
min   0.0015  -0.0550
25%   0.1029   0.0528
50%   0.2201   0.1595
75%   0.3555   0.4890
max   0.5000  10.1145

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.1263
L2   0.1263  1.0000

Annotation Correlation Matrix
       ANNOT
ANNOT    1.0

Annotation Matrix Column Sums
ANNOT    3093

Summary of Annotation Matrix Row Sums
count    83630.0000
mean         0.0370
std          0.1887
min          0.0000
25%          0.0000
50%          0.0000
75%          0.0000
max          1.0000
Analysis finished at Mon Jun 24 13:12:03 2024
Total time elapsed: 5.0m:53.97s
Done.