I've trying to use the polarize command but regardless of whether I pipe in the vcf or use the -i option, I always get the same error:
polarize: error: the following arguments are required: command
in this case, I used the command bcftools view pseudo_qual_dust_indel_fixedmissing_nodups_resorted_nodups2.vcf.gz | vcfdo polarize -f path/to/AMATA_finishedtohypo_renamedfinal_doubleAAmod.fasta
However I noticed this error occurs regardless of what command I try and use (e.g. treemix, pca, etc.). I'm wondering if it's an install issue because I initially had a NumPy version issue but I uninstall and reinstalled everything with pip and it seemed to install fine.
Thanks!
I've trying to use the polarize command but regardless of whether I pipe in the vcf or use the -i option, I always get the same error:
polarize: error: the following arguments are required: commandin this case, I used the command
bcftools view pseudo_qual_dust_indel_fixedmissing_nodups_resorted_nodups2.vcf.gz | vcfdo polarize -f path/to/AMATA_finishedtohypo_renamedfinal_doubleAAmod.fastaHowever I noticed this error occurs regardless of what command I try and use (e.g. treemix, pca, etc.). I'm wondering if it's an install issue because I initially had a NumPy version issue but I uninstall and reinstalled everything with pip and it seemed to install fine.
Thanks!