I am working on the NGS data by using some galaxy tools and I do not know many things on bioinformatics. The aim of my project is to type KIR genes at the allelic level. Those genes are very polymorphic like HLA genes. Now, I used BWA-MEM to align my illumina paired end reads to the human reference genome hg19 and try to visualized them on IGV but I do not know which galaxy tool should I use after to identify the different alleles for each gene. I read on the internet that after alignment, the next step is the calling variant but i do not know what tool for that...
Thank u in advance,