Make results report to save as xlsx sheets (full, filtered, peptides)

Make results report to save as xlsx sheets (full, filtered, peptides)

Usage

filter_variants(
  vr,
  ...,
  min_cov = 2,
  min_af = 0.05,
  pass = TRUE,
  sample = NULL,
  chrs = NULL
)

Arguments

vr

A VRanges object from `readVcfAsVRanges`

...

Force filters by name (ignored)

min_cov

Minimum number of reads to span the ALT allele

min_af

Minimum allele frequency of the ALT allele

pass

Whether to only include softFilterMatrix PASS

sample

Only include if in `sampleNames(vr)`

chrs

Either "default" or a character vector of chromosome names