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At the moment, users have to do null checks themselves, ie if you look for gnomAD < 0.01 you need to add an or gnomAD is NULL - except there's no easy way to make the AND/OR etc work nicely here.
Wou…
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There is a bug here: https://github.com/broadinstitute/gnomad_methods/blob/019865838f993841a540e0b29d8d2f3b1333b1b8/gnomad/utils/vep.py#L788
The `most_severe_consequence` field is a top level `vep`…
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A great tool! Is it possible to use the Genome Aggregation Database (gnomAD) instead of ExAC?
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prmac updated
2 months ago
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For example, variant `14-76135756-T-C`, which is found at https://gnomad.broadinstitute.org/variant/14-76135756-T-C?dataset=gnomad_r2_1, is missing in table `gnomad.annotation_v3`.
Querying for thi…
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## Describe the issue
Missing upstream cHGVS nomenclature for LDLR RefSeq transcript NM_000527.5.
Given variant 19-11200108-A-G, we'd expect a cHGVS nomenclature of c.-117A>G when using the RefSeq…
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Dear Prof. Wang,
I notice "hg38_gnomad_genome.txt" have multiple allele frequency in different population. I want to use this file to annotate my SNPs, however, I only want to show "gnomAD_genome_…
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In a recent case a known duplication was estimated as being 1000 basepair shorter than previously called. This resulted in annotsv missmatch to dbvar and gnomad which caused the variant to loose 6 poi…
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Dear developer,
I found gnomad database is not read successfully in sbs_counter.R, more specifically,
`gnomad
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Hi Xihao,
Thanks for your useful tool! And I've met some problems really confused me:
1. I noticed that allele frequencies of gnomAD and 1000G are contained in FAVOR full database but not in FAV…