diff --git a/RGBEPP.d b/RGBEPP.d index 54da3d4..9aab996 100644 --- a/RGBEPP.d +++ b/RGBEPP.d @@ -340,7 +340,7 @@ void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string // Variant calling using bcftools string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", referFasta, inputBam]; string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string]; - string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", referFasta, "-Oz"]; + string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", referFasta, "--check-ref", "s", "-Oz"]; string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf]; executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]); } diff --git a/RGBEPP_refmix.d b/RGBEPP_refmix.d index e13dc63..b1636f1 100644 --- a/RGBEPP_refmix.d +++ b/RGBEPP_refmix.d @@ -396,7 +396,7 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, stri // Variant calling using bcftools string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam]; string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string]; - string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"]; + string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "--check-ref", "s", "-Oz"]; string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf]; executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]); }