Everything that was available on Showcase should be available on RAP. It's a superset. If you find something missing, you can let us know, and we will fix it.
For imputed HLA, it's in RAP for sure since I analyzed it for my research before. If your application doesn't include this, you can request.
Hi guys, apologies for necro-ing a 3-year old thread but I could use some advice on this topic as well.
I have been trying to extract the HLA genotypes as a table on the RAP for an analysis. In order to do that I've been using the table exporter and have input a long version of the file that Chai Fungtammasan linked above (I.e. all fields in a column instead of in a row) as is required for the table exporter.
Unfortunately, this has not worked using either of FIELD-NAME or FIELD-TITLE in the table exporter. And my understanding is that UKB-FORMAT has to be in pXX_iYY_aZZ format (which doesn't exist for the HLA columns).
As such I am basically completely stumped with how to actually access the HLA genotypes for any downstream analyses.
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Everything that was available on Showcase should be available on RAP. It's a superset. If you find something missing, you can let us know, and we will fix it.
For imputed HLA, it's in RAP for sure since I analyzed it for my research before. If your application doesn't include this, you can request.
Note that you would also need this.
wget -nd biobank.ctsu.ox.ac.uk/crystal/crystal/auxdata/ukb_hla_v2.txt
This will give header for probability of each HLA in each sample.
Hi guys, apologies for necro-ing a 3-year old thread but I could use some advice on this topic as well.
I have been trying to extract the HLA genotypes as a table on the RAP for an analysis. In order to do that I've been using the table exporter and have input a long version of the file that Chai Fungtammasan linked above (I.e. all fields in a column instead of in a row) as is required for the table exporter.
Unfortunately, this has not worked using either of FIELD-NAME or FIELD-TITLE in the table exporter. And my understanding is that UKB-FORMAT has to be in pXX_iYY_aZZ format (which doesn't exist for the HLA columns).
As such I am basically completely stumped with how to actually access the HLA genotypes for any downstream analyses.
Any help here would be appreciated!
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