Vcf2FilteredGranges: extract SV variants from a sniffles VCF file by SVTYPE
In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
Description
Usage
Arguments
Value
Examples
Description
This method will extract SV variants as called by Sniffles
into a GRanges object with the variation length declared in the
SVLEN field, read support in RE, support type in SUPTYPE. The
variants will be filtered according to the svtype parameter
Usage
1
Vcf2FilteredGranges(vcfFile, svtype = "INS")
Arguments
vcfFile
is the path to the vcfFile to plot
svtype
defines one of INS/DEL/DUP
Value
a GRanges object describing the duplications
Examples
1
2
3
vcfFile <- system.file("extdata", "GM24385.nf7.chr20.vcf",
package = "nanopoRe")
Vcf2FilteredGranges(vcfFile, svtype = "INS")
sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.
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Description Usage Arguments Value Examples
Description
This method will extract SV variants as called by Sniffles into a GRanges object with the variation length declared in the SVLEN field, read support in RE, support type in SUPTYPE. The variants will be filtered according to the svtype parameter
Usage
1 | Vcf2FilteredGranges(vcfFile, svtype = "INS")
|
Arguments
vcfFile |
is the path to the vcfFile to plot |
svtype |
defines one of INS/DEL/DUP |
Value
a GRanges object describing the duplications
Examples
1 2 3 | vcfFile <- system.file("extdata", "GM24385.nf7.chr20.vcf",
package = "nanopoRe")
Vcf2FilteredGranges(vcfFile, svtype = "INS")
|
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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