run_annotate_vcf_pl: Wrapper function to annotate addition information

In YAPSA: Yet Another Package for Signature Analysis

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

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.