Hello,
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?
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dec986
1 answer
plink 1.07 does not support VCFs at all. It was last updated before the VCF format even existed.
plink 1.9 was explicitly designed to have maximal backward compatibility with plink 1.07, while adding VCF support; why are you still using 1.07?
Add "--recode vcf" (or "--recode vcf bgz" if you want gzipped output) to your command line. See https://www.cog-genomics.org/plink/1.9/data#recode .
plink 1.9 is still labeled as "beta" since there are a few (mostly CNV-related) very-rarely-used features in plink 1.07 which have not been either reimplemented or officially dropped; but for >99% of real use cases it can be considered to be finished.
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