filterVcfMuTect2 {PureCN} | R Documentation |
Function to remove artifacts and low confidence/quality calls from a
GATK4/MuTect2 generated VCF file. Also applies filters defined in
filterVcfBasic
.
filterVcfMuTect2(vcf, tumor.id.in.vcf = NULL, ignore = c("clustered_events", "t_lod", "str_contraction", "read_position", "fragment_length", "multiallelic", "clipping", "strand_artifact"), ...)
vcf |
|
tumor.id.in.vcf |
The tumor id in the VCF file, optional. |
ignore |
MuTect2 flags that mark variants for exclusion. |
... |
Additional arguments passed to |
A list with elements vcf
, flag
and
flag_comment
. vcf
contains the filtered CollapsedVCF
,
flag
a logical(1)
flag if problems were identified, further
described in flag_comment
.
Markus Riester
### This function is typically only called by runAbsolute via the ### fun.filterVcf and args.filterVcf comments. library(VariantAnnotation) vcf.file <- system.file("extdata", "example_vcf.vcf.gz", package="PureCN") vcf <- readVcf(vcf.file, "hg19") vcf.filtered <- filterVcfMuTect(vcf)