- fileName
character, represents an input VCF file (Bgzipped, with Tabix index)
- range
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index
- annoType
character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty.
- vcfColumn
character vector, which vcf columns to extract. It can be chosen from CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT and etc.
- vcfInfo
character vector, which should be tags in the INFO columns to extarct. Common choices include: DP, AC, AF, NS
- vcfIndv
character vector, which values to extract at individual level. Common choices are: GT, GQ, GD