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When I use Bio::SeqFeature::Tools::Unflattener to convert GenBank flat-feature-list to containment hierarchy,
```
$unflattener->unflatten_seq(-seq=>$seq, -use_magic=>1);
```
Everything is fine exce…
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The GFF3 specification is not really clear about how to treat CDS features of 1bp length that have a phase of 2 defined. According to
> The phase is one of the integers 0, 1, or 2, indicating the num…
satta updated
7 years ago
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We are trying to use genotyping arrays (Axiom) to get VCFs for demuxlet.
Are there any recommended steps / tutorials for SNP cleaning and filtering to optimise the demuxlet yield?
We are curren…
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## Feature request
### Tool(s) or class(es) involved
_Funcotator_
### Description
Need to add more indel test cases for HG38 for completeness.
The set of test cases should be:
{3' and…
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Wouldn't it be neat if one could go from protein position to genomic nucleotide position?
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Using SnpEff to predict sequence variant to gene relationships produces predicate terms from the Sequence Ontology (SO). Currently biolink mappings for Sequence Ontology terms are incomplete. https://…
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From https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM16193&product=CC
> donor subject is also heterozygous for an A>G transition at nucleotide 1226 in exon 9 of the GBA gene (122…
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We need to come up with some stats that we want to display for the gene_models files that are consumed.
Its pretty easy to do counts of field 3 and just report these, but should we do more?
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The current implementation outputs VAR and REF read counts for non-synonymous variants only. I would be great, as a user to have the option to output read-support counts for all variants. I've used Va…
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Given just how much information can be gleaned from these plots it would be incredibly useful if plots could be interactive (to allow for zooming, moving along a transcript structure, etc.). `plotly` …