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lifebit-ai / gwas

GWAS pipeline using SAIGE
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Encoding chromosomes as 'chr1' or '1' #91

Open kousathanas opened 3 years ago

kousathanas commented 3 years ago

Since GEL data encodes by default all chromosomes with prefix 'chr', we need to add argument to all plink commands so that the plink output format is compatible

--output-chr chrM

However, this will break cases with vcf files that encode chromosomes as integers. So it will be best to be able to pass this as an option. Same name, output-chr, with default set to chrM.

kousathanas commented 3 years ago

@mcamarad I will force set it now.