Convert SHAPEIT haps file to vcf
I’ve phased some sequencing using SHAPEIT, producing two files:
125QiPSC.haps
125QiPSC.log
I would now like to subset the file for my SNPs of interest. To achieve this, I’m first attempting to convert it to a vcf. The SHAPEIT manual suggests this can be done by –convert
However, when I try running this:
shapeit -convert
--input-haps "$DIR"/shapeit/125QiPSC
--output-vcf "$DIR"/shapeit/125QiPSC.vcf
I get the error message
Converter mode : unrecognised option '--output-vcf'
Am I doing something wrong?
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