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As briefly mentioned in #14, based on my own variant calling in our cancer dataset and the respective manuscripts, long-read somatic variant callers such as nanomonsv outperform current germline calle…
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### Description of feature
As mentioned here,
https://github.com/nf-core/sarek/pull/831#issuecomment-1313457016
the subway-map of the variant-callers seem to indicate that the variant-callers…
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Strelka2 (Illumina) seems to be a promising alternative to varscan2.
Mentioned in bcbio bcbio-nextgen issue 2345.
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### Description of the bug
Hi am working with the pipeline, in the test working fine. with samples do not report the VARIANT_CALLING, there is no error in the run.
How I can make that processes?
##…
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Small variant callers with LRs are being pushed out/updated, so we need to keep track of major updates and new comers
List of interesting ones
New
- [ ] [dipcall](https://github.com/lh3/dipcall…
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### Description of feature
Is it possible to publish GVCF file for every sample?
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While debugging a user issue (see [thread](https://groups.google.com/d/msg/google-genomics-discuss/r4_Kt2MITng/zEd723xdCwAJ)), we came across non-standard fields from VarScan2 (e.g. the "AD" field is …
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Hi there,
I'm looking for a good method to combine calls produced by short variant callers (50bp). Most structural variant merging tools are designed to merge SVs from different SV callers, and SNP…
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I am looking to use Varlociraptor to call SVs using candidates from several upstream callers (Delly, GRIDSS, Manta). Is there a recipe for how to configure Varlociraptor to do this?
Specifically, I…
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Hi,
I was wondering if you might be able to explain some very high QUAL scores in my VCFs?
I am calling variants from recent, high-quality bacterial (i.e., haploid) nanopore data.
This is the…