HLA typing¶
hlacaller
– Perform identification of highly polymorphic HLAs with human build 38 (hg38).
The recommended option is optitype
, using the OptiType caller.
Also supports using the bwa HLA typing implementation with bwakit
For typing either with optitype or with bwakit, aligner
must be set to bwa
.
aligner: false
+ hlacaller: optitype
in the template yaml gives a warning whan attempting to create a project yaml,
and errors out when running bcbio, issue 3252.