I'm running the command
plink-1.07-x86_64/plink --file ZZQDBCZE.chrX.vcf.gz --make-bed --set-hh-missing --out tmp --noweb
but this is outputting a bed file, which I can't use, as I need a VCF.
I either need a way to convert this to tmp.bed to VCF, or a way for plink to output tmp.vcf.
I've tried https://raw.githubusercontent.com/chapmanb/bcbb/master/nextgen/scripts/plink_to_vcf.py but I'm having difficulties converting, because the bx.seq library can't be loaded, even with bx installed.
How can I get this tmp.vcf?