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

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AF = (alt_count / (ref_count + alt_count))

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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.

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<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

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:

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Chromosome is a string matching a reference contig.

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Start and end values are zero-based, half open intervals.

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BAF is a floating point value.