aboutsummaryrefslogtreecommitdiff
path: root/tools
diff options
context:
space:
mode:
Diffstat (limited to 'tools')
-rw-r--r--tools/facets-call.nix7
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}
'';
}