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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB
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To improve variant calling efficiency the genome is split up into chromosomes and scaffolds. Then variant calling takes place for each region (chromosome or scaffold) separately. The scaffolds for the…
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hi, was wondering if the RNA-seq SNV variant calling for RNA-seq data is performed during the pipeline? If not, can this be added into future version?
https://gatk.broadinstitute.org/hc/en-us/artic…
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I have an unusual case where I have a variant in the vcfdist summary VCF which has a truth BD of FN and a query BD of FP.
Here is the vcfdist entry (with some context). The variant of interest is P…
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## Description:
Add MarkDuplicates to the DNA pipeline as well based on pipeline diagrammed from Broad Institute at:
* https://github.com/broadinstitute/gatk-docs/blob/master/gatk3-methods-and-a…
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https://mp.weixin.qq.com/s/BkP19EMHfCzytBd8EbFYVw
ixxmu updated
2 months ago
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Evidences:
https://github.com/cov-lineages/pango-designation/commit/0910a303d6fcafbde56874c80ca2f0f7ccf55a3c#commitcomment-117867742
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https://mp.weixin.qq.com/s/uzjYcJ08D-Y-sDGgUVk26w
ixxmu updated
3 months ago
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Hi,
For my 250x genome (after BQSR and indel realignment) has 4 million PASS variants.
Is that normal? That seems like too much.
Anything else that you do standard to pre-filter the variants to…
gevro updated
8 months ago
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### Description of feature
Hi,
It would be great if we could run Mutect2 in multi-sample mode for increased sensitivity and better concordance among samples. ~~For reference, there is a WDL implem…