run_annotate_vcf_pl {YAPSA} | R Documentation |
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 |
|
in_anno_track_file_type |
Type of the file |
in_data_CHROM.field |
String indicating which column of
|
in_data_POS.field |
String indicating which column of
|
in_data_END.field |
String indicating which column of
|
Return zero if no problems occur.
NULL