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# GREGoR next steps
## Use Case:
> As a GREGoR analyst, in order to `discover genotype to phenotype associations`, I would like to compare [CAF](https://github.com/ga4gh/va-spec/blob/1.x/sche…
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Dear
I am trying to do allelic analysis Hic data getting same error G2 is mapping reads are zero and iced normalisation step getting error. I used bellow command to run analysis. non allelic analysi…
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Hello,
We’re benchmarking against HG002 within Tier 1 regions using the HiFi sequel [data from HPRC](https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0). We’re getting good recall but low…
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### Description
As documented in #93, vcztools view is not running as fast as bcftools view on real genome data. I reproduce the performance data below.
This issue tracks understanding the perfo…
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Hello VG Team, I am currently working with the HPRC pangenome and aiming to construct a VCF file that highlights the differences between the two haplotypes (hap1 and hap2) of the HG002 sample. Specifi…
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Hi @reimand0 ,
I am getting an error, when trying to run ActiveDriveWGS using following command:
```
ActiveDriverWGS.res[[i]] = ActiveDriverWGS(mutations = ActiveDriverWGSInfo[[i]], elements = …
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**What is your question?**
@eblerjana I am working on reconstructing a haploid haplotype using the imputed genotypes from PanGenie. Currently, I am using the following commands:
```bash
PanGenie …
gsc74 updated
1 month ago
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Hi,
I am new to using bcftools +liftover, I want to liftOver from hg38 to hg19.
However, I get the error:
"Error: the reference allele GT does not match the reference NN at..."
I converted my …
ktg25 updated
2 months ago
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The rule annotate_vep does not run before annotate_esm.
After the checkpoint prescore, the snakemake pipeline directly runs annotate_esm.
It says that inside the snakefile, the input of annota…
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Hi, we have some R9 data that turn out to be a bit challenging. So we'd appreciate any suggestions.
We know that technically speaking, DV natively support only R10 data. And for R9, the recommended p…