Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations.

ABSTRACT: Cancer genome sequencing has led to important discoveries such as the identification of cancer genes. However, challenges remain in the analysis of cancer genome sequencing. One significant issue is that mutations identified by multiple variant callers are frequently discordant even when using the same genome sequencing data. For insertion and deletion mutations, oftentimes there is no agreement among different callers. Identifying somatic mutations involves read mapping and variant calling, a complicated process that uses many parameters and model tuning. To validate the identification of true mutations, we developed a method using k-mer sequences. First, we characterized the landscape of unique versus non-unique k-mers in the human genome. Second, we developed a software pa

SUBMITTER: Lee H 

PROVIDER: S-EPMC7727745 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature