Remove indexing step, IMPUTE5 outputs an index

atgu · Feb 27, 2024 · 53f5102 · 53f5102
1 parent ba7a435
commit 53f5102
Showing 1 changed file with 0 additions and 9 deletions.
diff --git a/gwaspy/imputation/impute5_impute.py b/gwaspy/imputation/impute5_impute.py
@@ -1,7 +1,5 @@
 __author__ = 'Lindo Nkambule'
 
-import argparse
-import hail as hl
 import hailtop.batch as hb
 import hailtop.fs as hfs
 import pandas as pd
@@ -68,13 +66,6 @@ def imputation(
  """
  )
 
- j.command(f"""
- bcftools index {j.imputed_chunk['chunk.bcf']} \
- --output {j.imputed_chunk['chunk.bcf.csi']} \
- --threads {ncpu}
- """
- )
-
  return j
 
  def concatenate_imputed_chunks(