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Fix ref_allele_mismatch in liftover_expr for indel variants #273

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Fix ref_allele_mismatch in liftover_expr for indel variants #273

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8cbbb5a
fix liftover_expr
mkanai Nov 18, 2020
5f27570
add CHANGELOG
mkanai Nov 18, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
* Add reference genome to call of `has_liftover` in `get_liftover_genome` [(#259)](https://github.com/broadinstitute/gnomad_methods/pull/259)
* Added fix for MQ calculation in `_get_info_agg_expr`, switched `RAW_MQ` and `MQ_DP` in calculation [(#262)](https://github.com/broadinstitute/gnomad_methods/pull/262)
* Fix for error in `default_lift_data` caused by missing `results` field in `new_locus` [(#270)](https://github.com/broadinstitute/gnomad_methods/pull/270)
* Fix for incorrect `ref_allele_mismatch` error in `liftover_expr` when the original reference allele has more than one bp [(#273)](https://github.com/broadinstitute/gnomad_methods/pull/273)

## Version 0.4.0 - July 9th, 2020

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4 changes: 3 additions & 1 deletion gnomad/utils/liftover.py
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Expand Up @@ -98,7 +98,9 @@ def liftover_expr(
original_locus=locus,
original_alleles=alleles,
locus_fail_liftover=hl.is_missing(lifted_over_locus),
ref_allele_mismatch=lifted_over_locus.result.sequence_context()
ref_allele_mismatch=lifted_over_locus.result.sequence_context(
after=hl.len(alleles[0]) - 1
)
!= lifted_over_alleles[0],
)

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