Can Plink 1.07 set-hh-missing output VCF?

Question

[dec986]

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?

Answer 1

[chrchang523]

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?

[dec986]

~/Scripts/plink1.9/plink --vcf ZZQDBCZE.chrX.vcf.gz --set-hh-missing --out tmp --recode vcf is the correct answer to my question

[chrchang523]

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.

[Lemire]

you need: --recode vcf

[dec986]

I kept seeing beta for Plink 1.9, which made me think that it's not ready