Description Usage Arguments Value Examples
Import a VCF directly into MTseeker
1 |
x |
character, list or dataframe for file name of VCF(and BAM) |
gzip |
Is the input gzipped? (FIXME: autodetect this) |
biscuit |
Is the input VCF from biscuit? (FALSE) |
verbose |
Print all messages during progress? (TRUE) |
an MVRangesList
1 2 3 4 5 6 7 | library(MTseekerData)
VCFdir <- system.file("extdata", package="MTseekerData")
VCF <- file.path(VCFdir, list.files(VCFdir, pattern="*.vcf.gz$"))
mvr <- importVCF(VCF)[[1]]
mvr$FILTER <- ifelse(totalDepth(mvr) >= 20, "PASS", ".")
mvr$PASS <- mvr$FILTER == "PASS"
filterMT(mvr)
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