prohlatype
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hammerlab
Probabilistic HLA typing
When running `make`, the following error appears: ``` File "src/lib/fastq.ml", line 76, characters 24-29: Error: The function applied to this argument has type ?init:(int -> unit) -> ?finalize:(unit -> unit)...
it's better to add `update apt-get` in line 36 of `src/scripts/run-example-docker.sh` ``` RUN sudo apt-get ``` without this line, i got some error like this: ``` E: Failed to fetch...
In particular the fall through to `float`s in ParPMM might be problematic.
Example, PGV has read-size of 125, so maybe we'd want a `--split-by 75,50` argument.
Probably more relevant when joining per-loci graphs.
Cf. [Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping](https://www.ncbi.nlm.nih.gov/pubmed/26319908/) (2015)
One thought: ImmPort has a lot of vaccine studies w/ HLA type and RNA-Seq data (maybe some have germline WES?)
### Oxford Nanopore - [NA12878](https://github.com/nanopore-wgs-consortium/NA12878) WGS data ### PacBio - PGV001 patients