The quality control of cancer somatic mutations is of great significance in tumor genomics. It helps to eliminate false positive mutations arisen during the sequencing process, thereby improving the efficiency and accuracy of downstream analysis. Here, we developed an R package CaMutQC, for the quality control and selection of cancer somatic mutations. It offers both common and customized strategies for the filtration of cancer somatic mutation based on the MAF data frame, which are able to select key somatic mutations related to tumorigenesis. In addition, we believe that the union of mutations returned by multiple variant caller contains more true positive somatic mutations than that from a single variant caller or the intersection of multiple callers. The package, source code and documents are freely available through Github (https://github.com/likelet/CaMutQC)
In R console, enter
For now, there are three main functional modules in CaMutQC. The
first section is to filter cancer somatic mutations through common
strategies, and the following section offers users customized filtration
criteria based on cancer types. CaMutQC is also capable of measuring TMB
(Tumor Mutational Burden) through various methods. Required input of
most functions in CaMutQC can be obtained by applying
vcfToMAF function on VCF files.
MAF data frame with special labels from CaMutQC will be returned after each filtration. And a filter report will be provided, giving detailed and organized result information.