TP53_SNP-calling

This pipeline is designed to analyze TP53 custom amplicon NGS data, performing variant calling and validating calls with a R-based workflow. For SNP validation we adopted 2 validiation pipelines: Fisher's exact test on Variant allele frequency (VAF) and Error modelling procedure based on distribution transformation.
Both procedures need a custom count-database generated from wild-type (WT) samples. We test the efficiency of this workflow with a database of 362 WT patients. All the scripts were used for data analysis in the paper titled "Small TP53 Mutated sub-clones predict short survival in Chronic Lymphocytic Leukemia" (unpublished)