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add checkpoint option to get_qc_mt #437

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Merged
merged 4 commits into from
Jan 25, 2022
Merged

add checkpoint option to get_qc_mt #437

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e13f5b4
add checkpoint
klaricch Jan 25, 2022
7ec4484
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9 changes: 8 additions & 1 deletion gnomad/sample_qc/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,7 @@ def get_qc_mt(
filter_segdup: bool = True,
filter_exome_low_coverage_regions: bool = False,
high_conf_regions: Optional[List[str]] = None,
checkpoint_path: Optional[str] = None,
) -> hl.MatrixTable:
"""
Create a QC-ready MT.
Expand All @@ -147,6 +148,7 @@ def get_qc_mt(
:param filter_segdup: Filter segmental duplication regions
:param filter_exome_low_coverage_regions: If set, only high coverage exome regions (computed from gnomAD are kept)
:param high_conf_regions: If given, the data will be filtered to only include variants in those regions
:param checkpoint_path: If given, the QC MT will be checkpointed to the specified path before running LD pruning. If not specified, persist will be used instead.
:return: Filtered MT
"""
logger.info("Creating QC MatrixTable")
Expand Down Expand Up @@ -179,7 +181,12 @@ def get_qc_mt(
)

if ld_r2 is not None:
qc_mt = qc_mt.persist()
if checkpoint_path:
logger.info("Checkpointing the MT and LD pruning")
qc_mt = qc_mt.checkpoint(checkpoint_path, overwrite=True)
else:
logger.info("Persisting the MT and LD pruning")
qc_mt = qc_mt.persist()
unfiltered_qc_mt = qc_mt.unfilter_entries()
pruned_ht = hl.ld_prune(unfiltered_qc_mt.GT, r2=ld_r2)
qc_mt = qc_mt.filter_rows(hl.is_defined(pruned_ht[qc_mt.row_key]))
Expand Down