README.md

In steverozen/DBSverify: Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

DBSverify

This is a beta version.

DBSverify stands for "Doublet Base Substitution verify". A "Doublet Base Substitution" is the simultaneous mutation of adjacent bases, for example mutations from TA to GT and from TC to AA, which are often caused by the carcinogen aristolochic acid.

The main function is Read_DBS_VCF_and_BAMs_to_verify_DBSs. This function reads a VCF (variant call format) file containing somatic DBS mutations and examines the supporting reads in the corresponding tumor and normal BAM files to assess whether each DBS is likely real, i.e. arose at one time on a single chromosome. This is as opposed to being two adjacent single base mutations on homologous chromosomes, or adjacent mutations that occurred on the same chromosome but at detectably different times. Many somatic mutation callers do not call DBSs at all, and those that do sometime make obvious errors, such as calling DBSs that consist of a germline SNP next to a somatic single base mutation.

The main function is Read_DBS_VCF_and_BAMs_to_verify_DBSs if you have a VCF with already-called DBSs. If you have a variant caller that does not call DBSs you can use Read_SBS_VCF_and_BAMs_to_verify_DBSs to combine adjacent SBSs to be analyzed as DBSs. The output of Read_DBS_VCF_and_BAMs_to_verify_DBSs is a new VCF file with an assessment of whether each DBSs is likely real or not.

To install

remotes::install_github("steverozen/DBSverify")

steverozen/DBSverify documentation built on Dec. 23, 2021, 5:34 a.m.