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humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data
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Cut ties to specific build? #20

Open keiranmraine opened 6 years ago

keiranmraine commented 6 years ago

Would it be possible to break the hard coded link to human GRCh38 and allow users to provide a set of reference data at execution time rather than embedding it in the image?

If it's possible to provide documentation as to how to generate the reference files this would make the tool both backwards and forwards compatible. We specifically would like GRCh37 supported in the short term (in our case without a chr prefix).

I'm happy to do testing of the resulting changes.

RachelKarchin commented 6 years ago

GRCh37 support would make this package so much more useful! Many of the datasets my group works with still use the older assembly.

tmhmxg59 commented 6 years ago

Please forgive my naïveté, but could someone suggest steps to use a GRCh37 aligned BAM? Like is it best to start with fq and realign or is there an easier way?

tmhmxg59 commented 5 years ago

In my hands, the provided get-reads script worked well for conversion from GRCh37 to GRCh38.

https://github.com/humanlongevity/HLA/issues/35