B-Allele Frequency Output
B-Allele frequency (BAF) output is enabled by default in germline and somatic VCF and gVCF runs.
The BAF value is equal to either AF or (1 – AF), where
| • | AF = (alt_count / (ref_count + alt_count)) |
| • | BAF = 1 – AF, only when ref base < alt base, order of priority for bases is A < T <G < C < N |
For each small variant VCF entry with exactly one SNP alternate allele, the output contains a corresponding entry in the BAF output file.
| • | <NON_REF> lines are excluded |
| – | ForceGT variants (as marked by the "FGT" tag in the INFO field) are not included in the output, unless the variant also contains the "NML" tag in the INFO field. |
| – | Variants where the ref_count and alt_count are both zero are not included in the output. |
BAF Options
--vc-enable-baf
Enable or disable B-allele frequency output. Enabled by default.
BAF Output
The BF generates are BigWig-compressed files, named <output-file-prefix>.baf.bw and <output-file-prefix>.hard-filtered.baf.bw. The hard-filtered file only contains entries for variants that pass the filters defined in the VCF (ie, PASS entries).
Each entry contains the following information:
Chromosome Start End BAF
Where:
| • | Chromosome is a string matching a reference contig. |
| • | Start and end values are zero-based, half open intervals. |
| • | BAF is a floating point value. |
