Easy script to run HLA typing tools on a batch of BAM files
- arcasHLA
- Specifically this fork that fixed some issues with the container and reference
- OptiType
- T1K
docker and docker compose are reqired to run the tools
clone the repository
git clone https://github.com/VergaJU/hla_tiping.git
create data directory:
cd hla_typing
mkdir data
copy the BAM files into data
run ./hla_typing.sh:
Run HLA typining with arcasHLA, OptiTyie and T1K.
Syntax: scriptTemplate [-i|t|h|]
options:
t number of threads. Default: 8
o output directory. Default: hla_typing_out
s single or paired end. Default: single
h Print this Help.