HLA type results are disappear in Genotype Imputation HLA

[asangphukieo]

I noticed that the format of Genotype Imputation HLA output has changed!

1. variant position and allele are used for the variant name instead of RS ID
2. HLA typing result are disappear in chr6.dose.vcf.gz and chr6.info.gz files

How can I get these information back?

Many thanks. Best,

[asangphukieo]

I found that this issue occur when submit the job with API script only.

#Example API command
curl -H "X-Auth-Token: $TOKEN" \
    -F "files=@input.vcf.gz" \
    -F "refpanel=apps@multiethnic-hla-panel-4digit-v2@1.0.0" \
    -F "build=hg19" \
    -F "input-phasing=eagle" \
    -F "population=mixed" \
    https://imputationserver.sph.umich.edu/api/v2/jobs/submit/minimac4

The result looks normal when I submit on web browse.

I think it is better to make the system consistent.

[seppinho]

Hi, MIS provides several worfklows via Run: "Genotype Imputation (Minimac4)" vs "Genotype Imputation HLA (Minimac4)". Your API example above uses the Minimac4 workflow.

[asangphukieo]

Thank you for your clarification

https://imputationserver.sph.umich.edu/api/v2/jobs/submit/minimac4

changes to

https://imputationserver.sph.umich.edu/api/v2/jobs/submit/imputationserver-hla

works now