run_annotate_vcf_pl {YAPSA} | R Documentation

## Wrapper function to annotate addition information

### Description

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.

### Usage

    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"
    )

### Arguments

`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.

### Value

Return zero if no problems occur.

### Examples

     NULL

[Package YAPSA version 1.18.0 Index]