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Add coverage_mt option to annotate_sex which takes an optional precomputed coverage MT to use for ploidy imputation instead of remaking it. #484

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Merged
merged 3 commits into from
Oct 5, 2022
Merged

Add coverage_mt option to annotate_sex which takes an optional precomputed coverage MT to use for ploidy imputation instead of remaking it. #484

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b15062a
Add option to `annotate_sex` to use a precomputed coverage MT for ref…
jkgoodrich Sep 14, 2022
d79c83e
Merge branch 'jg/annotate_sex_add_frac_hom_alt_option' of https://git…
jkgoodrich Sep 14, 2022
0c90186
Merge branches 'jg/annotate_sex_add_coverage_mt_option' and 'jg/annot…
jkgoodrich Sep 21, 2022
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25 changes: 19 additions & 6 deletions gnomad/sample_qc/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -339,6 +339,7 @@ def annotate_sex(
variants_filter_segdup: bool = True,
variants_filter_decoy: bool = False,
variants_snv_only: bool = False,
coverage_mt: Optional[hl.MatrixTable] = None,
compute_x_frac_variants_hom_alt: bool = False,
compute_fstat: bool = True,
infer_karyotype: bool = True,
Expand Down Expand Up @@ -395,6 +396,7 @@ def annotate_sex(
exist for GRCh38.
:param variants_snv_only: Whether to filter to only single nucleotide variants for variants only ploidy estimation
and fraction of homozygous alternate variants on chromosome X. Default is False.
:param coverage_mt: Optional precomputed coverage MatrixTable to use in reference based VDS ploidy estimation.
:param compute_x_frac_variants_hom_alt: Whether to return an annotation for the fraction of homozygous alternate
variants on chromosome X. Default is False.
:param compute_fstat: Whether to compute f-stat. Default is True.
Expand Down Expand Up @@ -470,12 +472,23 @@ def annotate_sex(
ref_keep_contigs,
)
if is_vds:
ploidy_ht = hl.vds.impute_sex_chromosome_ploidy(
hl.vds.filter_intervals(mtds, ref_keep_locus_intervals),
calling_intervals=included_intervals,
normalization_contig=normalization_contig,
use_variant_dataset=False,
)
if coverage_mt is not None:
ploidy_ht = hl.vds.impute_sex_chr_ploidy_from_interval_coverage(
coverage_mt.filter_rows(
hl.is_defined(included_intervals[coverage_mt.row_key])
& hl.literal(ref_keep_contigs).contains(
coverage_mt.interval.start.contig
)
),
normalization_contig=normalization_contig,
)
else:
ploidy_ht = hl.vds.impute_sex_chromosome_ploidy(
hl.vds.filter_intervals(mtds, ref_keep_locus_intervals),
calling_intervals=included_intervals,
normalization_contig=normalization_contig,
use_variant_dataset=False,
)
ploidy_ht = ploidy_ht.rename(
{
"x_ploidy": "chrX_ploidy",
Expand Down