From c16f68ee65adebcaa788837c87538ebcb6be434b Mon Sep 17 00:00:00 2001 From: LindoNkambule Date: Wed, 5 Feb 2025 15:53:04 -0500 Subject: [PATCH] outputs from GLIMPSE2_phase and GLIMPSE2_ligate are automatically indexed --- gwaspy/imputation/glimpse2_impute.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/gwaspy/imputation/glimpse2_impute.py b/gwaspy/imputation/glimpse2_impute.py index 83688b2..05a09f1 100644 --- a/gwaspy/imputation/glimpse2_impute.py +++ b/gwaspy/imputation/glimpse2_impute.py @@ -236,8 +236,6 @@ def glimpse2_impute_phase( --threads 4 \ --output {j.imputed_phased['bcf']}""") - j.command(f"""bcftools index -f {j.imputed_phased['bcf']} --output {j.imputed_phased['bcf.csi']} --threads {ncpu}""") - return j # 7. Ligate imputed chunks @@ -272,7 +270,6 @@ def ligate_chunks( j.command(f'echo "{imp_chunk_bcf_names}" > chunk_list.txt') j.command(f"""GLIMPSE2_ligate --input chunk_list.txt --output {j.ligated['bcf']} --threads {ncpu}""") - j.command(f"""bcftools index {j.ligated['bcf']} --output {j.ligated['bcf.csi']} --threads {ncpu}""") b.write_output(j.ligated, f'{out_dir}/glimpse/{output_vcf_name}_{chrom}.phased.imputed')