4.6. jsa.seq.annovcf: Annotate a vcf file¶
jsa.seq.annovcf: reads annotations from a gff file and annotates a vcf file (i.e., identify the functional of variation).
jsa.seq.annovcf is included in the Japsa package. Please see check the installation page for instructions.
4.6.1. Synopsis¶
jsa.seq.annovcf: Annotate variation in a vcf file using annotation from gff file
4.6.2. Usage¶
jsa.seq.annovcf [options]
4.6.3. Options¶
--gffin=s GFF file (default=’-‘) --upstream=i Add upstream (default=‘0’) --downstream=i Add downstream (default=‘0’) --output=s Name of output file, - for standard out (default=’-‘) --vcf=s Name of vcf file (REQUIRED) --help Display this usage and exit (default=’false’)