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# Context
Genetics etl dag described by the image below
should be possible to execute in two modes:
- run wi…
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Hello,
I’ve been using hap.py to benchmark two VCF files, but I keep encountering the following warning:
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/IMPORT_FAIL" is invalid, forcing Nu…
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## Describe the issue
Some BND variants are missing vep annotations, while the rest have them.
## Additional information
### System
- VEP version: 113
- VEP Cache version: 113
### Full VEP…
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Hello,
I would like to assign VCF file founders directly to a pedigree rather than randomly assigning them to founders.
Is there an internal way to do so? Or do I need to do this manually?
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Hello!
Many than for great package!
I wanted to ask how can extract vcf with info score from hla prediction output?
cl
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### Need
As a user, I want clear outputs. At the moment variant files are a mix of vcf and bcf, some indexed and some not, some compressed and some not.
### Suggested approach
Standardise output va…
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I am currently performing imputation on 23 chromosomes in vcf.gz files on my server. However, after imputation, I only obtained .vcf.gz files and did not get INFO.gz like others.
This is the comman…
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## Describe the issue
I am getting the following error and I've narrowed it down to a single line VCF:
```
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/Utils/Variati…
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Good evening,
`ngsPool` provides `poolSFS.R`, a script which estimates a one dimensional SFS from the `SAF.GZ` output file. Is it possible for other software to read pairs of "sample allele frequen…
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Dear bcftools :
I attempted to use bcftools to generate haplotype sequences using the phased.vcf (from HiPhase), but the process was unsuccessful. Are there alternative solutions available? Below is …