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It's time to make a new release this issue will track what needs to be done. Please add any essential (and only essential) updates as comments to this issue:
+ [x] update clinvar
+ [x] update CADD…
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I thought this would be interesting to have, as described in:
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php
…
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Long TODO lists don't get done.
We are trying to keep an issue open if a real effort is happening to resolve it.
The below priority list gives a sense of where bcbio is heading in the next two rele…
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Hi everyone,
I have received this error several times when running bcbio with a PON for mutect. It looks like too many instances are trying to access this file? I'm not sure what is causing this or…
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Edit: despite the title this link list now contains all kinds of reference material for benchmarking/normal-filtering SV (including CNV) calls on a population level as well on single sample (mostly ce…
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problem, installing from scratch on our HPC fails while trying to install a perl packages:
```
Encountered problems while solving:
- package perl-encode-locale-1.05-pl526_6 requires perl >=5.26.…
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I've been trying to run mity report on my vcf that I called with mity call. However, there are no results in the excel file that correspond to the vcfanno step. Looking further into it, it appears tha…
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Hi,
I'm trying to annotate a VCF with only 248 variants using the gnomad genomes VCF as annotation and it takes about 2 hours to run. Both the input VCF and the annotation VCF are indexed with tab…
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I'm hitting this repeatedly when trying to load VCFs that have been merged via `bcftools merge` then normalized and decomposed via `vt` and then annotated via `vcfanno`. Note that each of these had b…