VCFfile: Prepare VCF file for filtering.
In BartBroeckx/Mendelian: Variant Analysis for Mendelian Disorders

Description Usage Arguments Details Author(s) Examples

VCFfile should be used to process VCF files prior downstream analysis with any other function.

1	VCFfile(x, sample, filter, value)

`x`	the VCF file to be processed.
`sample`	specify the column name containing the variant info for the sample of interest.
`filter`	logical, should the variants have a certain quality value in the 7th mandatory column of the VCF format?
`value`	optional, which variants should be retained? (e.g. PASS)

This function should be used to process VCF files to make them compatible for further filtering. If wanted, a preliminary filtering can be performed by specifiying filter = TRUE and a value in "value". As VCF files can contain variant information from >1 sample, the column name of the sample of interest should be specified.

Bart Broeckx

# test 1: filter = TRUE
  x <- test
  sample <- "V10"
  filter <- TRUE
  value <- "PASS"
  VCFfile(x,sample, filter, value)

  # test 2: filter = FALSE
  x <- test
  sample <- "V10"
  filter <- FALSE
  VCFfile(x,sample, filter)