View source: R/parse_vcf_output.R
Parse a VCF input to return a data frame with standardised fields across callers to use for caller comparison. It only works with germline calls and for VCF from the following callers: GATK3 MuTect2, VarScan2 and VarDict.
1 | parse_vcf_output(vcf_path, sample_name, caller)
|
vcf_path |
path to where the '.vcf' file for one sample is saved. |
sample_name |
character. Sample name of the current 'vcf' file. |
caller |
character. One of 'mutect', 'vardict' or 'varscan'. |
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