R/mutect2_gatk3_8.R

In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

mutect2_gatk3_8 <- function(GenomeAnalysisTK='/software/debian-8/bio/gatk-3.8/GenomeAnalysisTK.jar',
                            refgen='/imppc/labs/lplab/share/marc/refgen/hg38/hg38.fa',
                            tumor,
                            normal,
                            cosmic='/imppc/labs/lplab/share/marc/refgen/hg38/mutect2/CosmicMuts.gatk.vcf.gz',
                            dbsnp='/imppc/labs/lplab/share/marc/refgen/hg38/mutect2/00-common_all.vcf',
                            output){

  system(paste('java',
               '-jar',
               GenomeAnalysisTK,
               '-T MuTect2',
               '-R', refgen,
               '-I:tumor', tumor,
               '-I:normal', normal,
               '--cosmic', cosmic,
               '--dbsnp', dbsnp,
               '--contamination_fraction_to_filter 0.02',
               '-o', output,
               '--output_mode EMIT_VARIANTS_ONLY',
               '--disable_auto_index_creation_and_locking_when_reading_rods'))
}