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Right now we can get the same position twice, with two different rsids, where one rsid has one allele as reference and the other has the other. Or the same phenomena but as strand flips.
```
(base…
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Hello,
I use MutSigCV analyzed my mutation data. It shows some error. I think maybe something is wrong with my input file. Could you please tell me how to revise it? The error is:
Error using gp…
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Hi @johanneskoester !
Can you recommend a grammar for Germline variant calling?
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**Submitting author:** @lincoln-harris (Lincoln Harris)
**Repository:** https://github.com/czbiohub/cerebra
**Version:** v1.1.0
**Editor:** @lpantano
**Reviewers:** @betteridiot, @afrubin
**Managing …
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This request was created from a contribution made by ABours on May 29, 2020 18:23 UTC.
Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360067695771-GenotypeGvcfs-has-formatting-issues-…
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Hi,
when calling VEP with the dbNSFP plugin as follows
/data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep \
--species homo_sapiens \
--input_file test.vcf \
--output_file ouput…
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**Submitting author:** @lincoln-harris (Lincoln Harris)
**Repository:** https://github.com/czbiohub/cerebra
**Version:** v1.2.0
**Editor:** @lpantano
**Reviewer:** @betteridiot, @afrubin
**Archive:** …
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## Bug Report
### Affected tool(s)
GenotypeGVCFs
### Affected version(s)
4.0.2.0
### Description
After running GenomicsDBImport which takes a short time, GenotypeGVCFs takes a really long time to…
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I updated from 4.0.4.0 to 4.0.6.0 and noticed either a memory bug or spike in GenotypeGVCF.
Based on https://github.com/EvanTheB/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4.simple…
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The rsIDs of marker variants are explicitly declared for markers from ALFRED, Chen 2019, Hiroaki 2015, and Staadig 2019. This is not the case for van der Gaag 2018. The code to cross-reference marker …