I am trying to run PAINTOR with two populations EUR and AFR. The sign/direction of the z-score value in Locus1.LD1.processed and Locus1.LD2.processed are systematically flipped compared to the original Locus1 file after running CalcLD_1KG_VCF.py. Is this normal ?
Example output
Locus
CHR POS RSID A1 A0 ZSCORE.P1 ZSCORE.P2
2 127841586 rs10205454 A G -0.577123478575 0.837899543378996
Locus1.LD1.processed
CHR POS RSID A1 A0 ZSCORE.P1 ZSCORE.P2
2 127841586 rs10205454 A G 0.577123478575 0.837899543378996
Locus1.LD2.processed
CHR POS RSID A1 A0 ZSCORE.P1 ZSCORE.P2
2 127841586 rs10205454 A G -0.577123478575 -0.837899543379
Hello,
I am trying to run PAINTOR with two populations EUR and AFR. The sign/direction of the z-score value in Locus1.LD1.processed and Locus1.LD2.processed are systematically flipped compared to the original Locus1 file after running CalcLD_1KG_VCF.py. Is this normal ?
Example output Locus CHR POS RSID A1 A0 ZSCORE.P1 ZSCORE.P2 2 127841586 rs10205454 A G -0.577123478575 0.837899543378996 Locus1.LD1.processed CHR POS RSID A1 A0 ZSCORE.P1 ZSCORE.P2 2 127841586 rs10205454 A G 0.577123478575 0.837899543378996 Locus1.LD2.processed CHR POS RSID A1 A0 ZSCORE.P1 ZSCORE.P2 2 127841586 rs10205454 A G -0.577123478575 -0.837899543379
Example code python PAINTOR_V3.0/PAINTOR_Utilities/CalcLD_1KG_VCF.py \ --locus RunDirectory/Locus1 \ --reference ../../../example/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \ --map_file ../../../example/integrated_call_samples_v3.20130502.ALL.panel \ --position POS \ --effect_allele A1 \ --alt_allele A0 \ --population EUR \ --out_name RunDirectory/Locus1.LD1 \ --Zhead ZSCORE.P1
Any feedback would be appreciated, Iris