filterVcfMuTect {PureCN} | R Documentation |
Function to remove artifacts and low confidence/quality calls from a MuTect
generated VCF file. Also applies filters defined in filterVcfBasic
.
This function will only keep variants listed in the stats file and those not
matching the specified failure reasons.
filterVcfMuTect( vcf, tumor.id.in.vcf = NULL, stats.file = NULL, ignore = c("clustered_read_position", "fstar_tumor_lod", "nearby_gap_events", "poor_mapping_region_alternate_allele_mapq", "poor_mapping_region_mapq0", "possible_contamination", "strand_artifact", "seen_in_panel_of_normals"), ... )
vcf |
|
tumor.id.in.vcf |
The tumor id in the VCF file, optional. |
stats.file |
MuTect stats file. If |
ignore |
MuTect 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.gz", package="PureCN") vcf <- readVcf(vcf.file, "hg19") vcf.filtered <- filterVcfMuTect(vcf)