KIRcaller is Python tool that implements our KIR3DS1/L1 genotyping method (publication under review). It works with BAM files that were created by aligning ExomeSeq or WGS reads to genome version hg19. If a different genome assembly was used for read alignment, it is mandatory to provide a custom GFF file that describes the relevant KIR3DS1/L1 regions (see KIR3DS1_L1.gff GFF file in the "data/" subfolder) for the corresponding genome assembly.
Requirements:
- Linux
- subread (http://subread.sourceforge.net/)
- Python 2.7
- Pandas (python module)
Installation:
callKIR3D.py and data/ including its contents need to be located in the same directory:
e.g. /home/$USER/KIRCaller
KIRcaller/
├── callKIR3D.py
├── data
└── KIR3DS1_L1.gff
featureCounts form the subread package should be located in your $PATH,
alternatively it can be specified via the -f or --featureCounts option.
Running the tool:
A simple run would be:
./callKIR3D.py -b /data/KIR/BAM -o KIR_geontyping.tsv
(tested in on CentOS Linux 7.5 using python 2.7.14, subread 1.6.0 and 1.6.1)