run_annotate_vcf_pl: Wrapper function to annotate addition information

Description Usage Arguments Value Examples

View source: R/interact_foreign.R

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

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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

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slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.