Man pages for Bio-Core/BioCore.Annotation
BioCore Variant Annotation Package

add_protein_change_column	Add protein change column.
add_read_depth_column	Add a read depth column to the ANNOVAR output dataframe.
add_sample_name	Add sample namel
add_snvid	Add SNVID
add_variant_allele_fraction_column	Add variant allele fraction (VAF) column to dataframe.
create_merged_data	Create merged data
create_recurrence_heatmap	Create recurrence heatmap
create_recurrence_table	Create a table of recurrently mutated genes.
create_variant_signature_barplot	Create the variant signature barplot
filter_annovar_data	Filter ANNOVAR data
filter_on_depth	Filter on depth.
filter_on_population	Filter on population data.
get_annovar_colnames	Get the ANNOVAR column names
get_annovar_files	Get a list of ANNOVAR files.
get_coding_mutations	Get coding mutations.
get_pyrimidine_change	Get pyrimidine change
get_read_depth	Get the read depth.
get_snv	Get single nucleotide variants (SNVs)
get_variant_allele_fraction	Get the variant allele fraction from the FORMAT string.
load_annovar_file	Load an ANNOVAR file.