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Hi @dancooke ,
I am experiencing an issues where Octopus seems to miss variant calls in very-high depth regions (2000-5000x and higher).
The parameters typically used are:
```
caller=cance…
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Hi @d-cameron.
Thanks for your software. I got now a vcf file but it's difficult to interpret when you have only breakpoints.
I have used the `StructuralVariantAnnotation` package and the code…
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Review of Medusa versus Phoenix calls in PCL patients by @sskerget identified a MYC mutation ~35% AF that was lost in the new pipeline. It is called by 2 callers (Mutect2 and Strelka2). It is called …
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hi, I am using DV 0.9 to find *de novo* variants in trios and so I am enriching for weird stuff.
I am sure your team is aware of some/all of these, but I'll document at least 1 case here for the rec…
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**Submitting author:** @chorscroft (Clare Horscroft)
**Repository:** https://github.com/chorscroft/zalpha
**Version:** v0.2.0
**Editor:** @lpantano
**Reviewers:** @juanvillada , @marcrr
**Archive…
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Hey guys!
Thanks for the great pipeline!
Has anybody checked the precision of RNA-seq variant calling since the introduction of gatk4?
Previously, with gatk 3x after rna-editing filtration it w…
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Hi everyone!
Do you have any recommendations for circulating tumor dna analysis?
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**Submitting author:** @mlindsk (Mads Lindskou)
**Repository:** https://github.com/mlindsk/molic
**Version:** v1.0.0
**Editor:** @csoneson
**Reviewer:** @jdeligt, @jkanche
**Archive:** 10.5281/zenodo.…
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Hi,
I am writing here to seek your opinion on using HapCUT2 to perform phasing genome of a plant that I am interested at. I have a plant genome that I am working on, genome size 400Mb, 11 chromosom…
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We'd like to provide support for other models of mutation. Here is a proposal for how to do this, in a two-stage protocol, that separates generating locations of the mutations (which can be done indep…