pyc1216 / hlaloh-pipeline

hla-typing by optitype & polysolver , detect loh by lohhla.

For test

cd test snakemake -s ../hla_loh.docker.smk loh_all -np

NOTE

data/

abc_complete.fasta

This is from polysolver(conda or docker build)

hla.dat

This is from LOHHLA(https://github.com/slagtermaarten/LOHHLA.git) /data/hla.dat

images/

polysolver.tar.gz

docker pull sachet/polysolver:v4 docker save -o images/polysolver.tar.gz sachet/polysolver:v4

lohhla.tar.gz

docker pull mleventhal/lohhla:latest docker save -o images/lohhla.tar.gz mleventhal/lohhla:latest