vcf_to_mutations_df: Helper function to read a vcf into the required format of mutations data frame
Description
Uses VariantAnnotation::readVcfAsVRanges to read the vcf file, which return variants
in a format that each row is one variant. If the vcf has multiple samples, the samples
will be appended by rows. Provide a sample_name to return only the variants belonging
to the sample of interest. Once you use this function, make sure that all the variants
are relevant. The function will only return SNVs.
Usage
vcf_to_mutations_df(vcf, sample_name = NULL, ...)
Arguments
vcf
the path to vcf file
sample_name
a character(1) when provided, return only variants from this sample
...
other options passed to VariantAnnotation::readVcfAsVRanges
# NOT RUN {vcf <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf_to_mutations_df(vcf, sample_name = "HG00096")
# }# NOT RUN {# }