Mutation Annotation tool for mutation pathogenicity classification To work with notebooks please use jupyter. First install dbnsfp_annotation package, then mutant. Models are attached to the repository.
python setup.py installOR
pip install -e .frommutant.classifierimportadd_mutant_annotation# example, annotate vcf, genome version hg19 (this vcf file are not attached)add_mutant_annotation('TCGA-A1-A0SB.vcf', file_type='vcf', genome_version='hg19', development_mode=True, method='predict_proba')
# example, annotate maf, genome version hg38add_mutant_annotation('TCGA-A1-A0SB.maf', file_type='maf', genome_version='hg38', development_mode=True, method='predict_proba')
# convert maf DNP to SNP and annotate, genome version hg38add_mutant_annotation('TCGA-A1-A0SB.maf', file_type='maf', genome_version='hg38', dnp_convert_info=True, method='predict_proba')
# After annotation you will get «DNP_Converted» column in your maf with True or False values,# where True means that DNP was converted to SNP while annotation,# False - DNP could not be converted to SNP because of for amino acid change it need in two or more changes in codon.