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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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Error when generating ld matrix using CalcLD_1KG_VCF.py #58

Open akhilpampana opened 2 years ago

akhilpampana commented 2 years ago

Hello,

I am running the LD matrix based on the code snippet you provided. Here is the code I am using

python CalcLD_1KG_VCF.py --locus overall_pval_chr1_rsid_0.01.tsv \ --reference ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \ --map integrated_call_samples_v3.20130502.ALL.panel \ --population EUR \ --Zhead Zscore \ --out_name chr1_eur_overall \ --effect_allele A1 \ --alt_allele A0 \ --pos pos

I am getting this warning/error.

/share/apps/rc/software/Anaconda3/2021.11/lib/python3.9/site-packages/numpy/lib/function_base.py:2642: RuntimeWarning: invalid value encountered in true_divide c /= stddev[:, None] /share/apps/rc/software/Anaconda3/2021.11/lib/python3.9/site-packages/numpy/lib/function_base.py:2643: RuntimeWarning: invalid value encountered in true_divide c /= stddev[None, :]

It would be of real help if you could help me resolve this issue?

Regards Akhil Pampana