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’)