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**Tools**
- [x] bwamem (no source update release)
- [x] bwa-mem2 - AJ
- [x] cnvnator (no source update release)
- [x] cyrius
- [x] expansionhunter (no source update release)
- [x] fastqc (no sou…
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Hello,
Thank you for your work on gvanno!
I have gotten gvanno working on my centOS 7 box, and the example annotation ran well. However, when I am trying to annotate a simple vcf file like the fol…
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Hi cravat team,
The 'POPAF' tag produces infinite values in Mutect2(gatk4) output and your program crashes on it. Maybe close/wontfix it for now. This is mainly to point other users in the right …
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Brent,
We are preparing a manuscript for resubmission and within we are providing a full, detailed pipeline which integrates tools from the Quinlan lab, including:
VCFAnno, VCF2DB, GEMINI.
VCF…
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These two changes were part of the Decemeber 2020 release of crg, but was missed out in crg2. This needs to be updated first to compare performance between crg2 and bcbio+crg pipelines.
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When the input VCF has no samples, the pipeline adds a "FORMAT" header somewhere along the way, leading to this error:
Unable to parse header with error: Your input file has a malformed header: The…
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Hi,
Can we map RNA-Seq data to hg38 with STAR? I have tried both stable and development versions. STAR directory is empty for both of the versions.
**Version info**
- bcbio version (`bcbio_nex…
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Hello,
Thank you for this nice tool.
I am trying to annotate my vcf with CADD using your tool. When I launch the vcfanno tool, a file is created.
In this new vcf file a line was added in the head…
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To whom this may concern,
I am trying to include multiple INFO field columns in the html report but for some reason it only prints values from the first column. Also the column header names are mis…
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**Hi,
Following the example here: https://brentp.github.io/vcfanno/examples/gff_sv/gff_sv/; I managed to carry out annotation of my vcf file using a gff file for the same isolate.
Conf and lua fil…