Question: Convert VCF to BGEN 1.3
2
gravatar for Vince
12 months ago by
Vince120
Montreal, Quebec, Canada
Vince120 wrote:

I have imputed genotype data from the Haplotyle Reference Consortium in VCF format, and would like to convert to BGEN 1.3 (or 1.2). I know that qctool version 2 support this, as does plink version 2.0.

I would like to inquire as to experiences anyone has had converting genotype probabilities (GP field in VCF) using these tools:

  1. Is one tool preferred over the other?
  2. Any caveats we should be aware of?

I would tend to use plink, as it is quite popular and actively developed, although the developers of qctool also developed the BGEN format, which may make it more ideal. I would assume these tools are equivalent for the task of converting VCF to BGEN, but your experience with this may suggest otherwise.

qctool plink bgen vcf • 890 views
ADD COMMENTlink modified 12 months ago by chrchang5234.9k • written 12 months ago by Vince120
2
gravatar for chrchang523
12 months ago by
chrchang5234.9k
United States
chrchang5234.9k wrote:

plink2 supports allelic dosages, not genotype probabilities. So if your VCF GP field says P(0/0)=0.2, P(0/1)=0.52, P(1/1)=0.28, plink2 will just save "dosage(1)=1.08", and then when it's asked to export to BGEN it'll encode the dosage as P(0/0)=0, P(0/1)=0.92, P(1/1)=0.08.

When this is fine, plink2 is a good choice. When this isn't good enough, use something like qctool.

ADD COMMENTlink written 12 months ago by chrchang5234.9k

Do you have link to the plink website where this is stated? This would he helpful.

ADD REPLYlink written 12 months ago by Vince120

Found it here, https://www.cog-genomics.org/plink/2.0/input, "Dosage import settings" section.

ADD REPLYlink written 12 months ago by Vince120
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