Recognize SURVIVOR simSV file #43

GooglingTheCancerGenome · Mar 31, 2020 · d733ffc · d733ffc
1 parent c746e05
commit d733ffc
Showing 1 changed file with 2 additions and 4 deletions.
diff --git a/scripts/R/vcf2bedpe.R b/scripts/R/vcf2bedpe.R
@@ -14,8 +14,6 @@ p <- add_argument(p, "-p", help="SVTYPE=INS if insertion length >= SV length * p
   type="numeric", default=0.7)
 p <- add_argument(p, "-l", help="Minimum SV length to consider", type="int",
   default=50)
-p <- add_argument(p, "-s", help="Is the input file from SURVIVOR simSV? TRUE/FALSE",
-  type="boolean", default=FALSE)
 
 # parse the command line arguments
 argv <- parse_args(p)
@@ -65,9 +63,9 @@ apply_svtype <- function(gr, p_inslen)
 
 sv_callset_vcf <- VariantAnnotation::readVcf(argv$i)
 
-if(argv$s)
+# handle SURVIVOR simSV SVTYPE <TRA> as TIGRA <CTX>
+if("TRA" %in% info(sv_callset_vcf)$SVTYPE & !("CT" %in% names(info(sv_callset_vcf))))
 {
-  # handle SURVIVOR simSV SVTYPE <TRA> as TIGRA <CTX>
   info(sv_callset_vcf)$SVTYPE[info(sv_callset_vcf)$SVTYPE=="TRA"] <- "CTX"
 }