Fixing human gatk4 var calling

EdinburghGenomics · Jul 1, 2019 · 6920bc1 · 6920bc1
1 parent a33c522
commit 6920bc1
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/analysis_driver/pipelines/human_variant_calling_gatk4.py b/analysis_driver/pipelines/human_variant_calling_gatk4.py
@@ -198,11 +198,11 @@ def stage(cls, **params):
                      output_vcf_file=hard_filter_indels.hard_filtered_vcf,
                      previous_stages=[hard_filter_snps, hard_filter_indels])
 
-    gender_val = stage(qc.GenderValidation, vcf_file=merge_hf.hard_filtered_vcf, previous_stages=[merge_hf])
+    sex_val = stage(qc.SexValidation, vcf_file=merge_hf.hard_filtered_vcf, previous_stages=[merge_hf])
 
     vcfstats = stage(qc.VCFStats, vcf_file=merge_hf.hard_filtered_vcf, previous_stages=[merge_hf])
 
-    final_stages = [contam, blast, geno_val, gender_val, vcfstats, verify_bam_id, samtools_depth, samtools_stat,
+    final_stages = [contam, blast, geno_val, sex_val, vcfstats, verify_bam_id, samtools_depth, samtools_stat,
                     gather_gcvf]
 
     output = stage(common.SampleDataOutput, previous_stages=final_stages, output_fileset='gatk4_human_var_calling')

diff --git a/etc/output_files.yaml b/etc/output_files.yaml
@@ -291,7 +291,7 @@ gatk4_human_var_calling:
         basename: '{sample_id}-chr22-vbi.selfSM'
         new_name: '{user_sample_id}-chr22-vbi.selfSM'
 
-    gender_call:
+    sex_validation:
         location: ['gatk4']
         basename: '{user_sample_id}_hard_filter.sex'
         new_name: '{user_sample_id}.sex'