read_vcf: Read and write VCF tables
In EricEdwardBryant/mutagenesis: Mutagenesis

Read and write VCF tables

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read_vcf(file, col_types = NULL, callback = NULL, chunk_size = 1e+06, ...)

write_vcf(vcf, file)

`file`	`[character(1)]` Path to VCF file. Supported file extensions: `.vcf`, `.vcf.gz`, `.vcf.bz2`. Compressed files are unzipped for the duration of the R session via R.utils::gunzip, or R.utils::bunzip2. `write_vcf` only supports `.vcf`.
`col_types`	`[col_spec\|character(1)\|NULL]` Either NULL, or a valid column specification (for more details, see readr::read_tsv). Defaults to only read the following expected VCF columns: - CHROM [character] - POS [integer] - ID [character] - REF [character] - ALT [character] - QUAL [double] - FILTER [character] - INFO [character]
`callback`	`[function(x, pos)\|NULL]` A function with arguments `x` and `pos` that takes a dataframe as `x` and returns a dataframe (`pos` is used internally). This is usefull for filtering or summarizing VCF files that are otherwise too big to read into memory. See readr::DataFrameCallback and readr::read_tsv_chunked for examples. Defaults to `NULL`.
`chunk_size`	`[integer(1)]` Number of lines to read for each chunk when using a callback. Defaults to `1e6`.
`...`	Arguments passed to readr::read_tsv, or readr::read_tsv_chunked if `callback` is not `NULL`.
`vcf`	`[vcf]` A VCF data frame. Simply a data frame with a `vcf` class and an attribute that contains VCF header information.