Integrated variant allele frequency analysis pipeline and R package: easyVAF.

ABSTRACT: Somatic sequence variants are associated with cancer diagnosis, prognostic stratification, and treatment response. Variant allele frequency (VAF), the percentage of sequence reads with a specific DNA variant over the read depth at that locus, has been used as a metric to quantify mutation rates in these applications. VAF has the potential for feature detection by reflecting changes in tumor clonal composition across treatments or time points. Although there are several packages, including Genome Analysis Toolkit and VarScan, designed for variant calling and rare mutation identification, there is no readily available package for comparing VAFs among and between groups to identify loci of interest. To this end, we have developed the R package easyVAF, which includes parametric and nonparamet

SUBMITTER: Hu J 

PROVIDER: S-EPMC10843735 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature