read_manta_vcf: Read Manta VCF
In pdiakumis/woofr: Helper R Functions for woof
read_manta_vcf R Documentation
Read Manta VCF
Description
Read main columns of interest from Manta VCF using bcftools or bedr
Usage
read_manta_vcf(vcf)
Arguments
vcf
Path to Manta VCF file (.vcf.gz or .vcf).
Details
Uses bcftools (https://samtools.github.io/bcftools/bcftools.html)
or bedr (https://cran.r-project.org/web/packages/bedr/index.html) to read
in the VCF file.
Value
A dataframe (tibble) with the following fields from the VCF:
chrom1: CHROM (remove chr prefix (if any) for hg38 compatibility)
pos1: POS | INFO/BPI_START
pos2: INFO/END | INFO/BPI_END
id: ID
mateid: INFO/MATEID
svtype: INFO/SVTYPE
filter: FILTER
af: BPI_AF
fmt_map: FORMAT
fmt_val: SAMPLE
pdiakumis/woofr documentation built on Jan. 4, 2024, 11:22 a.m.
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| read_manta_vcf | R Documentation |
Read Manta VCF
Description
Read main columns of interest from Manta VCF using bcftools or bedr
Usage
read_manta_vcf(vcf)
Arguments
vcf |
Path to Manta VCF file ( |
Details
Uses bcftools (https://samtools.github.io/bcftools/bcftools.html) or bedr (https://cran.r-project.org/web/packages/bedr/index.html) to read in the VCF file.
Value
A dataframe (tibble) with the following fields from the VCF:
chrom1:
CHROM(removechrprefix (if any) for hg38 compatibility)pos1:
POS|INFO/BPI_STARTpos2:
INFO/END|INFO/BPI_ENDid:
IDmateid:
INFO/MATEIDsvtype:
INFO/SVTYPEfilter:
FILTERaf:
BPI_AFfmt_map:
FORMATfmt_val:
SAMPLE
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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