diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 869e024..1b36cf6 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -313,7 +313,6 @@ def get_all_mhcI_alleles(wildcards): return values - ##### MHC CLASS II ##### def get_input_hlatyping_mhcII(wildcards): diff --git a/workflow/rules/germline.smk b/workflow/rules/germline.smk index 6759f44..317dfd6 100644 --- a/workflow/rules/germline.smk +++ b/workflow/rules/germline.smk @@ -15,7 +15,7 @@ rule get_gatk_vqsr_training_sets: message: "Downloading training sets for calling high confidence variants" log: - "logs/gatk_get_training)_sets.log" + "logs/gatk_get_training_sets.log" conda: "../envs/basic.yml" shell: @@ -133,9 +133,9 @@ rule merge_variants_htc_first_round: "../envs/bcftools.yml" shell: """ - bcftools concat -O z -a {input.vcf} -o {output} > {log} 2>&1 + bcftools concat --naive-force -O z {input.vcf} -o - | bcftools sort -O z -o {output} > {log} 2>&1 """ - + rule index_merged_variants_htc_first_round: input: "results/{sample}/{seqtype}/indel/htcaller/{group}_variants.1rd.vcf.gz"