GATK4 -Filter Mutect2 calls by orientation bias

Description

Additionally filter Mutect2 somatic variant calls for sequence context-dependent artifacts, e.g. OxoG or FFPE deamination.

Parameters

Details

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,

Output

References

This tool is based on the GATK4 package.

For instructions on citing GATK4, please see GATK FAQ