Question: Can Plink 1.07 set-hh-missing output VCF?
1
gravatar for dec986
6 weeks ago by
dec986230
United States
dec986230 wrote:

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?

plink • 95 views
ADD COMMENTlink modified 6 weeks ago by chrchang5237.1k • written 6 weeks ago by dec986230
1
gravatar for chrchang523
6 weeks ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

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 COMMENTlink modified 6 weeks ago • written 6 weeks ago by chrchang5237.1k

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

ADD REPLYlink written 6 weeks ago by dec986230

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by dec986230
1

you need: --recode vcf

ADD REPLYlink written 6 weeks ago by Lemire590
1

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.

ADD REPLYlink written 6 weeks ago by chrchang5237.1k
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