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### TL;DR
Why is the SV chr14_73,085,269_73,141,832_INV not annotated with the promoter 580535_pro (chr14_73,135,539_73,138,139) despite the promoter being fully within the SV region?
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Tha…
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Hi Brent,
I'm working on setting up a slivar pipeline with @jxchong; we have a number of annotation files that are bed formatted rather than vcf/bcf. Do you have a recommended tool for conversion? …
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### Description of feature
After Jasmine some filter steps should still be added.
1. A possibility to filter commonly occurring variants given through an input VCF
2. A way to hard filter based on…
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Hi Brent, I'm using SLIVAR on a trio VCF that has been annotated using VEP firstly and then passed to vcfanno (thank you!) for clinvar annotations.
My info field looks something like this:
ch…
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We currently show the gnomAD AF, but could we also get and display the count of homozygotes?
If we have this, could we also add this to the custom filter page?
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### Description of the bug
When using CADD, the number of VEP processes seems to be the square of the number of scatters of the genome. I expect it should instead be equal to the number of scatters, …
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Hi,
I am a newbie using Annovar and just encountered this. I have annotated a vcf file, following the instructions. I have noticed that CADD_phred has dots for some variants and numbers for others.…
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BALSAMIC adds annotations to VCFs from Swegen and loqusDB-clinical for SNV and SV.
Scout will be able to show the filter fields for these annotations in both SNV and SV views for cancer cases.
…
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The next `BALSAMIC` release `v13.x.x` (currently in `develop`) will include cancer germline and somatic loqusdb-observations/frequences annotations for SNVs and SVs. Similar to #4017, it will be nice …
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Is it, or would it be, possible to annotate with multiple CADD annotations file.
Since the Indels have to be calculated most of the times we have a file with the calculated CADD scores for the indel…