diff options
| -rw-r--r-- | tools/facets-call.nix | 7 |
1 files changed, 1 insertions, 6 deletions
diff --git a/tools/facets-call.nix b/tools/facets-call.nix index 021cacc..a736627 100644 --- a/tools/facets-call.nix +++ b/tools/facets-call.nix @@ -14,11 +14,6 @@ stage { name = "facets"; buildInputs = [ facets.app ]; buildCommand = '' - # Facets requires lexical sorting on the VCF files - grep '^#' ${vcf} > input.vcf - grep -v '^#' ${vcf} | LC_ALL=C sort -t $'\t' -k1,1 -k2,2n >> input.vcf || true - - # Now actually run facets - snp-pileup input.vcf $out ${concatStringsSep " " bams} + snp-pileup ${vcf} $out ${concatStringsSep " " bams} ''; } |