parsesnpeff: parse snpeff output into granges
In kevinmhadi/khtools: Making Mskilab Life Easier
parsesnpeff R Documentation
parse snpeff output into granges
Description
parse snpeff output into granges
expand all annotations into separate rows
Usage
parsesnpeff(
vcf,
id = NULL,
filterpass = TRUE,
coding_alt_only = TRUE,
geno = NULL,
gr = NULL,
keepfile = FALSE,
altpipe = FALSE,
debug = FALSE,
snpeffpath = "~/modules/SnpEff",
filters = "PASS,."
)
Arguments
vcf
path to snpeff vcf
pad
Exposed argument to skitools::ra.overlaps()
Value
GRangesList of breakpoint pairs with junctions that overlap removed
kevinmhadi/khtools documentation built on Jan. 16, 2025, 4:18 p.m.
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| parsesnpeff | R Documentation |
parse snpeff output into granges
Description
parse snpeff output into granges expand all annotations into separate rows
Usage
parsesnpeff(
vcf,
id = NULL,
filterpass = TRUE,
coding_alt_only = TRUE,
geno = NULL,
gr = NULL,
keepfile = FALSE,
altpipe = FALSE,
debug = FALSE,
snpeffpath = "~/modules/SnpEff",
filters = "PASS,."
)
Arguments
vcf |
path to snpeff vcf |
pad |
Exposed argument to skitools::ra.overlaps() |
Value
GRangesList of breakpoint pairs with junctions that overlap removed
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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