# Create new version HLA reference for VBSeq ###### tags: `c4lab` VBSeq Wang, YY., Mimori, T., Khor, SS. et al. HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel. Hum Genome Var 6, 29 (2019). https://doi.org/10.1038/s41439-019-0061-y http://nagasakilab.csml.org/hla/ ## Main changed I tested on 3.42.0 * Download specific IMGT/HLA version ``` bash git clone https://github.com/ANHIG/IMGTHLA HLA cd HLA git checkout 3420 cd .. ``` * Replace `hla_all_v2.fasta` to `HLA/hla_gen.fasta` * Replace `Allelelist_v2.txt` to `Allelelist.3420.txt` by ``` bash grep -v "#" HLA/Allelelist.3240.txt | sed 's/,/ /g' > Allelelist_3240.txt ``` ## TL;DR ``` sh cp HLA/hla_gen.fasta vbseq/hla_3420_gen.fasta grep -v "#" HLA/Allelelist.3240.txt | sed 's/,/ /g' > vbseq/Allelelist_3240.txt bwa index vbseq/hla_3420_gen.fasta bwa mem -t 30 -P -L 10000 -a vbseq/hla_3420_gen.fasta \ {name}.R1.fq.gz \ {name}.R2.fq.gz \ -o {name}.vbseq.sam java -jar vbseq/HLAVBSeq.jar vbseq/hla_3420_gen.fasta \ {name}.vbseq.sam \ {name}.vbseq.call.txt \ --alpha_zero 0.01 perl vbseq/parse_result.pl vbseq/Allelelist_3240.txt \ {name}.vbseq.call.txt | sort -k2 -n -r > {name}.vbseq.HLA.txt ```