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Add bi_allelic_only and snv_only options to get_qc_mt #471

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Merged
merged 2 commits into from
Jul 25, 2022
Merged

Add bi_allelic_only and snv_only options to get_qc_mt #471

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8fbc3b3
Add `bi_allelic_only` and `snv_only` options to `get_qc_mt`
jkgoodrich Jul 19, 2022
10d6945
Address review comments
jkgoodrich Jul 25, 2022
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13 changes: 11 additions & 2 deletions gnomad/sample_qc/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -109,6 +109,8 @@ def filter_rows_for_qc(

def get_qc_mt(
mt: hl.MatrixTable,
bi_allelic_only: bool = True,
snv_only: bool = True,
adj_only: bool = True,
min_af: Optional[float] = 0.001,
min_callrate: Optional[float] = 0.99,
Expand All @@ -126,16 +128,19 @@ def get_qc_mt(
"""
Create a QC-ready MT.

Keeps the following:
Has options to filter to the following:
- Variants outside known problematic regions
- Bi-allelic SNVs only
- Bi-allelic sites only
- SNVs only
- Variants passing hard thresholds
- Variants passing the set call rate and MAF thresholds
- Genotypes passing on gnomAD ADJ criteria (GQ>=20, DP>=10, AB>0.2 for hets)

In addition, the MT will be LD-pruned if `ld_r2` is set.

:param mt: Input MT
:param bi_allelic_only: Whether to only keep bi-allelic sites or include multi-allelic sites too.
:param snv_only: Whether to only keep SNVs or include other variant types.
:param adj_only: If set, only ADJ genotypes are kept. This filter is applied before the call rate and AF calculation.
:param min_af: Minimum allele frequency to keep. Not applied if set to ``None``.
:param min_callrate: Minimum call rate to keep. Not applied if set to ``None``.
Expand Down Expand Up @@ -178,6 +183,8 @@ def get_qc_mt(
min_inbreeding_coeff_threshold,
min_hardy_weinberg_threshold,
apply_hard_filters,
bi_allelic_only,
snv_only,
)

if ld_r2 is not None:
Expand All @@ -193,6 +200,8 @@ def get_qc_mt(

qc_mt = qc_mt.annotate_globals(
qc_mt_params=hl.struct(
bi_allelic_only=bi_allelic_only,
snv_only=snv_only,
adj_only=adj_only,
min_af=min_af if min_af is not None else hl.null(hl.tfloat32),
min_callrate=min_callrate
Expand Down