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### Description of feature
Is it possible to publish GVCF file for every sample?
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Hi Dr. Cullen,
I was wondering if there is a config.yaml file for Fca126_mat1.0 reference genome?
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Hello,
I have encountered a similar issue to ticket #502. I have been attempting to phase single genome files from targeted Pacbio sequencing, but unfortunately, no variants were phased. It appears t…
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## Bug Report
### Affected tool(s) or class(es)
GenotypeGVCFs with `-all-sites`
### Affected version(s)
- 4.2 through 4.6
### Description
We tried to run GenotypeGVCFs from GATK 4.5 with …
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Hi,
I am trying to run PEDDY for the first time.
I have gVCF output from GATK exomesinglesample wdl
The format of the vcf is like this:
```
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT F_001 F…
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Review of Quinn Wai work:
- Why not gVCF?
- CIViC match sanity check
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hi wang
i crossmap gvcf 2 hg38
```
CrossMap.py gvcf /disk/reference/liftover_ref/hg19ToHg38.over.chain M248.g.vcf.gz /storage/data/reference/update_gatk_v0/Homo_sapiens_assembly38.fasta crossmap_…
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Hi.
I'm trying to merge ~500 gvcf files, but they are failing at the validation step:
[88309] [2021-03-10 04:32:58.726] [GLnexus] [info] Created sample set *@555
[88309] [2021-03-10 04:32:58.72…
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EDIT (from @cjfields):
Modules checklist:
- [x] alignment (accelerated bwa)
- [ ] ~BQSR (optional?) (EDIT: Won't be implemented. It should be possible to use GATK-based BQSR.)~
- [x] DNAseq (SN…
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Hello, thank you for building this useful R package. I have made various plots using alignment files and vcf metrics using the `PHGmetrics` constructor object `metData`. I was wondering if there is an…