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Hi,
I am using Bayestyper to genotype my yeast strains after the clustering step but I'm getting an assertion failure error. I ran `bayestyper genotype` with the --noise-genotyping parameter due to…
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I am struggling to completely understand the differences of the outputs in AA and AC and how to translate this to presenting the results of the analysis:
If I have an individual sample which appears …
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Hi,
I am using Bayestyper to genotype SNPs of HG002 but I'm getting an assertion failure error. The reference SNPs are fetched from file processed by GIAB using freebayes.
The commands I used a…
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I added a commit (194f40ee00bedfcbd4fec277e6b0f38a3ae3803f) with a suggested change, feel free to modify or roll back as need be.
The change suggests requiring variants be submitted using one of a di…
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The vocabulary HGNC (Human Gene Nomenclature (European Bioinformatics Institute) is listed on the Athena vocabulary site https://athena.ohdsi.org/vocabulary/list as an optional download, but when sele…
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**Describe the bug**
When looking at variant 1 of the VariantValidator truth set, I tried updating to a MANE variant.
I got a strange delins in the MANE transcripts which is a simple substitution …
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### Background:
SPDI (Sequence Position Deletion Insertion) nomenclature and HGVS (Human Genome Variation Society) nomenclature are two standards that when used correctly, can uniquely identify seq…
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This issue is for brainstorming, not an immediate request to "fix" this, as it's something that requires careful thought.
One of the things I love about VV is that is checks variants thoroughly whe…
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Hi,
I am using `GATK ASEReadCounter` from GATK 4.2.0.0 and encounter the error
`A USER ERROR has occurred: More then one variant context at position: chrX:2774793`
As I googled, that means …
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from what i can tell, only one of the two genes in a gene fusion is curated in oscar's database. for example, selection of therapy_variant.id = 724 gives:
+--------------------+--------------------…