load_variants: Load a variant call file. Allowed types are either call_stats...

In bmannakee/batcaver:

Description

The function is generally internal, but is exported to help the user in debugging input

Usage

load_variants(vcf, file_type = "vcf", reference, sample_name)

Arguments

file_type	vcf or call_stats default is vcf
reference	/path/to/reference Path to the reference genome used to call variants. Must be a BSGenome object
sample_name	The sample name of the tumor in the vcf file
variant_file	/path/to/variant/file

Value

Data frame with 5 columns: chr, start, end, ref_allele, alt_allele

Examples

# Load variant calls from MuTect2
## Not run: 



## End(Not run)

bmannakee/batcaver documentation built on Jan. 6, 2020, 5:29 a.m.