run_annotate_vcf_pl: Wrapper function to annotate addition information
In slw287r/yapsa: Yet Another Package for Signature Analysis

Description Usage Arguments Value Examples

Wrapper function to the perl script annotate_vcf.pl which annotates data of a track stored in file_B (may be different formats) to called variants stored in a vcf-like file_A.

run_annotate_vcf_pl(
  in_data_file,
  in_anno_track_file,
  in_new_column_name,
  out_file,
  in_data_file_type = "custom",
  in_anno_track_file_type = "bed",
  in_data_CHROM.field = "CHROM",
  in_data_POS.field = "POS",
  in_data_END.field = "POS"
)

`in_data_file`	Path to the input vcf-like file to be annotated
`in_anno_track_file`	Path to the input file containing the annotation track
`in_new_column_name`	String indicating the name of the column to be created for annotation.
`out_file`	Path where the created files can be stored.
`in_data_file_type`	`custom` for vcf-like
`in_anno_track_file_type`	Type of the file `in_anno_track_file` containing the annotation track.
`in_data_CHROM.field`	String indicating which column of `in_data_file` contains the chromosome information.
`in_data_POS.field`	String indicating which column of `in_data_file` contains the position information.
`in_data_END.field`	String indicating which column of `in_data_file` contains the end information if regions are considered.