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### Description of the bug
We have run Sarek pipeline v3.1.2 on 3 WGS batches, including around 2500 samples, using the GATK.GRCh38 reference genome from iGenomes and mostly default parameters (see t…
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## Description
During the investigation of MAF results we noticed that Genotype is only showing the MAF variant calls and not the sequence calls from our bcf file. Examples of this is described in …
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I am trying to create a react component that integrates IGV for ROS_Cfam_1.0 but I get a console error Error loading IGV: TypeError: Cannot read properties of undefined (reading 'cytobandURL') below t…
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### Description of the bug
This is arguably a problem with genmod and there is a bug report https://github.com/Clinical-Genomics/genmod/issues/130, but I hope you don't mind that I report it here.
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`phase_rare` is failing while attempting to index the output, with errors like the following printed to stderr across all chunks:
```
[W::bcf_record_check] Bad BCF record at 28101822: Invalid CONT…
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This bug was originally raised by @iimpulse
For reference, the query: https://api-dev.monarchinitiative.org/api/bioentity/gene/MGI:98297/variants?fetch_objects=true&start=0&rows=10&facet=true&face…
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see this nice list:
https://github.com/seandavi/awesome-cancer-variant-databases
related to #15, @dnahotline, @mbrush @stuppie @pnrobinson can you prioritize these and make a Dipper/Wikidata/BioTh…
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Hi bcftools team,
I have a conceptual question about mpileup and I think the -d flag is either being weird or I'm misunderstanding how it works. I am using bcftools v. 1.18, and the .bam file in q…
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## Describe the issue
When you run VEP against a VCF record with a reference that is different from the fasta sequence, the consequences are calculated against provided base, while HGVS is calcualt…
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Status: ACTIVE
Platform contact; TBD
Researcher contact: TBD (will ask Matt Wheeler)
Next steps: requires moving BAM files into AWS hot storage at SRA for DRS accessibility. This use case also re…