The Allogenomics Scoring Tool is a software that estimates the allogenomics mismatch score, given genotypes for two DNA samples (Mesnard L et al, PeerJPrePrint). We have found that the allogenomics mismatch score correlates with graft function post-transplantation in two cohorts of kidney transplant recipients. This page provides resources (software and data) associated with the manuscript.
- The source code is available here: Allogenomics Scoring Tool BitBucket repository
- You can also download the latest binary distribution:
The following command line will process an input VCF file to produce scores for each transplant pair:
java -jar allogenomics-1.1.7-scoring-tool.jar -i input.vcf.gz \ -p pairs-definition.pairs -a protein_coding.gtf \ -t secreted+transmembrane.tsv -o secreted+transmembrane-scores.tsv
java -jar allogenomics-1.1.7-scoring-tool.jar -—help
will print usage information.
Note that the tool assumes the VCF format was produced with Goby (discover-sequence-variants mode), followed by annotation with the Variant Effect Predictor. Other VCF format flavors may also be compatible as long as the file includes genotype information and VEP annotations in an INFO field called ‘VariantEffectPrediction’ (see example header file in VCF_files_input/headers.vcf). Goby VCF files can be generated from read files with the NYoSh Analysis Workbench (open-source) or with GobyWeb.