Fig. 6

Using a “post-annotation” block to compute new annotations derived from existing annotations. a As described in the text, computing this post-annotation assumes that the “exac_total” and “exac_alts” fields have been extracted (via the AN and AC fields in the ExAC VCF) from the annotation file using standard annotation blocks. The AC field returns an array of alternative alleles for the variants in the annotation file that match a given variant in the query VCF. b In this post-annotation block, we calculate the alternative allele frequency in ExAC (“exac_aaf”) using “exac_alts [1]” as the numerator because in this example we calculate the alternative allele frequency based on the first alternative allele. c An example of a post-annotation block that calls a function (af_conf_int) in an external lua script (Additional file 2) to compute the lower bound of the allele frequency confidence interval based upon counts of the alternative allele and total observed alleles. d An example invocation of vcfanno that annotates a BGZIP-compressed VCF file (example.vcf.gz) using the configuration file described in panels (a–c) (red), together with the lua script file (blue) containing the code underlying the af_conf_int function