Additionally filter Mutect2 somatic variant calls for sequence context-dependent artifacts, e.g. OxoG or FFPE deamination.
Additionally filter Mutect2 somatic variant calls for sequence context-dependent artifacts, e.g. OxoG or FFPE deamination.
This tool is complementary to FilterMutectCalls and if run, should be run after FilterMutectCalls. The tool requires the pre-adapter detailed metrics calculated by Picard CollectSequencingArtifactMetrics and specification of the base substitution(s) to consider for orientation bias. For a given base substitution specified with the --artifact-modes argument, the tool considers both the forward and reverse complement for filtering. That is, specifying --artifact-modes 'G/T' means the tool considers G to T and A to C artifacts for filtering.
The metrics from CollectSequencingArtifactMetrics give a global view across a sample's genome that empowers decision making in ways site-specific analyses cannot. The detailed metrics measure orientation bias for all three-base contexts and help determine whether variant filtering for a sequence context is necessary.
The most common artifact to consider for filtering is the OxoG (8-Oxoguanine) artifact. OxoG artifacts stem from oxidation of guanine to 8-oxoguanine, which results in G to T transversions. If samples were derived from histological slides, then consider the FFPE (formalin-fixed paraffin-embedded) artifact. FFPE artifacts stem from formaldehyde deamination of cytosines, which results in C to T transitions.
Based on GATK4 FilterByOrientationBias tool. For more detailed information, see GATK documentation,
This tool is based on the GATK4 package.
For instructions on citing GATK4, please see GATK FAQ