Orientation Bias Filter
The orientation bias filter is designed to reduce noise typically associated with the following:
| • | Pre-adapter artifacts introduced during genomic library preparation (eg, a combination of heat, shearing, and metal contaminates can result in the 8-oxoguanine base pairing with either cytosine or adenine, ultimately leading to G→T transversion mutations during PCR amplification), or |
| • | FFPE (formalin-fixed paraffin-embedded) artifact. FFPE artifacts stem from formaldehyde deamination of cytosines, which results in C to T transition mutations. |
The orientation bias filter can only be used on somatic pipelines. To enable the filter, set the --vc-enable-orientation-bias-filter option to true. The default is false.
The artifact type to be filtered can be specified with the --vc-orientation-bias-filter-artifacts option. The default is C/T,G/T, which correspond to OxoG and FFPE artifacts. Valid values include C/T, or G/T, or C/T,G/T,C/A.
An artifact (or an artifact and its reverse compliment) cannot be listed twice. For example, C/T,G/A is not valid, because C→G and T→A are reverse compliments.
The orientation bias filter adds the following information.
| • | ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> |
| • | ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> |
| • | ##FORMAT=<ID=OBC,Number=1,Type=String,Description="Orientation Bias Filter base context"> |
| • | ##FORMAT=<ID=OBPa,Number=1,Type=String,Description="Orientation Bias prior for artifact"> |
| • | ##FORMAT=<ID=OBParc,Number=1,Type=String,Description="Orientation Bias prior for reverse compliment artifact"> |
| • | ##FORMAT=<ID=OBPsnp,Number=1,Type=String,Description="Orientation Bias prior for real variant"> |