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uint indelN; "number of indels"
uint indelS; "indel spaces"
uint alignB; "bases Aligned"
uint matchB; "aligned bases that match"
uint mismatchB; "aligned bases…
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Hi,
for SNVs, one can easily calculate confidence intervals for the dN/dS ratios per gene using the `geneci()`, which is really useful. However, it only calculates confidence intervals for SNV classe…
loipf updated
11 months ago
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Hi, I am trying to get a reasonable alignment in a region which has some tandem repeats, flanked by non-repetitive sequence. I can get good (enough) results in the tandem region using these parameters…
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Hi Tamsen,
I've been testing validation datasets using Pisces and the results are very promising, however I have run into an issue where Pisces will complain about indels which have no anchor, stemmi…
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Hello,
Let's say I want to call a consensus with two conditions:
1. Don't assume reference when variant is missing, print N.
2. At heterozygous sites, print the longer allele, if they are the s…
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This is linked to #15 as it leads to production of ambiguous prgs (multiple paths give rise to same sequence)
Clustering code can conclude that there is no meaningful clustering of a set of sequenc…
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Hi,
In the "All SNVs and INDELs" search option, would it be possible in future updates to add the field corresponding to the Inheritance model in the search results and as a search filter (genetic mo…
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Hello,
I was reading the methods of splice graph construction and was wondering if PsiCLASS uses quality scores at any point? Also, are indels, substitutions and soft-clippings used? I was thinking…
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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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Hi @freeseek ,
Thanks a lot for the tools provided in this repo.
I have a question with regard to the munging plugin, it appears that indel variants are systematically flagged when the alleles are …