diff --git a/rules/Analysis/MGMT.rules b/rules/Analysis/MGMT.rules index a4207d12f524efe4ad9e456bfd47677146173e8a..71932b225efd396896a172afb64a94a4bcdf12a4 100644 --- a/rules/Analysis/MGMT.rules +++ b/rules/Analysis/MGMT.rules @@ -131,7 +131,6 @@ rule ANALYSIS_MG_VARIANT_CALLING: ### run_mpileup {input[0]} {input[1]} $VCF_MPU samtools mpileup -uf {input[0]} {input[1]} | bcftools view -vcg - > $VCF_MPU - wait bgzip -c $VCF_MPU > $VCF_MPU.gz tabix -f -p vcf $VCF_MPU.gz @@ -145,8 +144,6 @@ rule ANALYSIS_MG_VARIANT_CALLING: bgzip -c $VCF_PLT > $VCF_PLT.gz tabix -f -p vcf $VCF_PLT.gz - - ### "Merging outputs " ## Must remove colons from the contig names in upstream steps. Unable to merge the variants