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In oeder to create gene-level group file from typically formatted VCF file, one may use the following utility
In oeder to create gene-level group file from typically formatted VCF file, one may use the following utility
epacts makegroup --vcf [input-vcf] --out [output-group-file] --format [epacts, annovar, chaos or gatk] --nonsyn
${EPACTS_DIR}/epacts makegroup --vcf [input-vcf] --out [output-group-file] --format [epacts, annovar, chaos or gatk] --nonsyn
The above command create a file [output-group-file] containing a list of missense and nonsense variants per each gene. To incorporate different types of functional annotations, use --type option as follows
The above command create a file [output-group-file] containing a list of missense and nonsense variants per each gene. To incorporate different types of functional annotations, use --type option as follows
epacts makegroup --vcf [input-vcf] --out [output-group-file] --format [epacts, annovar, chaos or gatk] --type [function_type_1] --type [function_type_2] ...
${EPACTS_DIR}/epacts makegroup --vcf [input-vcf] --out [output-group-file] --format [epacts, annovar, chaos or gatk] --type [function_type_1] --type [function_type_2] ...
Type 'epacts makegroup -man' for the detailed documentation
Type 'epacts makegroup -man' for the detailed documentation
