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MRCIEU / gwas2vcf

Convert GWAS summary statistics to VCF
MIT License
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no 'shape' argument in main.py #82

Closed GGboy-Zzz closed 3 months ago

GGboy-Zzz commented 3 months ago

Hi, I wanted to convert a GWAS catalog summary statics to the VCF format, yet I countered the error 'main.py: error: unrecognized arguments: shape'. I tried to downgrade the numpy version according to #74 image But that doesn't seem to be the problem. My code is as follows, looking forward to your reply！

SumStatsFile=GWAS_database/rawdata/XiongZ_31763980.txt.gz ParamFile=GWAS_database/reference/parameters_file ID='facial shape' RefGenomeFile=GWAS_database/reference/FASTA/human_g1k_v37.fasta DbSnpVcfFile=GWAS_database/reference/dbSNP/dbsnp.v153.b37.vcf.gz VcfFileOutPath=GWAS_database/outputs/facial_shape.vcf aliasFile=GWAS_database/reference/alias/alias-b37.txt miniconda3/envs/gwas2vcf/bin/python gwas2vcf/main.py \ --data ${SumStatsFile} \ --json ${ParamFile} \ --id ${ID} \ --ref ${RefGenomeFile} \ --dbsnp ${DbSnpVcfFile} \ --out ${VcfFileOutPath} \ --alias ${aliasFile}

GGboy-Zzz commented 3 months ago

I know what happened, Sorry to bother you！