expecting mixcr output from bulk RNAseq. CDR3A will be ignored. {sample_name}.clonotypes.TRB.txt is the expected file name.
python prep_GLIPH2_mixcr.py dir_mixcr
before the execution, collect *.genotype.json in a directory.
#!/bin/bash
set -x
mkdir -p arcasHLA
cut -f 1 gdc_manifest.2020-01-18.txt | tail -n +2 | while read line
do
echo $line
cp ${line}/VIRTUS_1.2.1_kz0.3/arcasHLA/humanAligned.full.csv arcasHLA/${line}.csv
cp ${line}/VIRTUS_1.2.1_kz0.3/arcasHLA/humanAligned.genotype.json arcasHLA/${line}.genotype.json
done
then,
python prep_GLIPH2_arcasHLA.py test
See http://50.255.35.37:8080/tools and download refs.
cd test
irtools.centos -c GLIPH2.params.txt
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