Changed Glimpse2Imputation QC metrics output format

broadinstitute · Sep 17, 2024 · 67dbba2 · 67dbba2
1 parent 5599798
commit 67dbba2
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/GlimpseImputationPipeline/Glimpse2Imputation.wdl b/GlimpseImputationPipeline/Glimpse2Imputation.wdl
@@ -325,7 +325,9 @@ import pandas as pd
 hl.init(default_reference='GRCh38', idempotent=True)
 vcf = hl.import_vcf('~{imputed_vcf}', force_bgz=True)
 qc = hl.sample_qc(vcf)
-qc.cols().flatten().rename({'sample_qc.' + col: col for col in list(qc['sample_qc'])}).export('~{output_basename}.qc_metrics.tsv')
+qc_pd = qc.cols().flatten().rename({'sample_qc.' + col: col for col in list(qc['sample_qc'])}).to_pandas()
+qc_pd = qc_pd.rename(columns={'s': 'sample_id'})
+qc_pd.to_csv('~{output_basename}.qc_metrics.tsv', sep='\t', index=False, float_format='%.4f')
 EOF
         python3 script.py
     >>>