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Hi!
during our dependency check the following came along:
One or more dependencies were identified with vulnerabilities that have a CVSS score greater than or equal to '9,0':
haplogrep-3.2.1.jar…
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Could Haplogrep perhaps be added to Galaxy (even though no one else will probably ever use this ever)? If so, possibly some kind of file converter will probably need to be added, as I don't be lieve H…
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Dear all,
Is it possible to run haplogrep2 on non-human species to identify haplogroups? If not, what additional information would I need if I wanted to set this up on another model organism?
Apolo…
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I have a VCF file which is a merge of a set of VCF files and hence some columns have all values set to `.`.
```
##source=DRAGEN_SNV
##bcftools_mergeVersion=1.16+htslib-1.16
##bcftools_mergeComma…
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I am unable to find in the documentation how exactly a phylotree should be specified in the `--phylotree` argument of `haplogrep classify`.
For example, all the following fail:
```
--phylotree=…
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Hi,
I have created a merged vcf file using **vcf-merge** tool for ~1000 samples.
When I am trying to provide this file as an input for the haplogrep, it is showing the following error:
Start Cla…
VGDEC updated
3 years ago
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Hello,
I am using VCF files (created by Mutect) as input for haplogrep2 and I am having issues with processing indels, which are longer than 1-bp.
I had to change "285 GAA -> G" to two variants: …
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I have already sequenced a batch of yeast data and would like to use Haplocheck to detect contamination in the WGS data. I note that the examples mentioned in _Contamination detection in sequencing st…
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When trying to annotate with Haplogrep2, it complains because INFO contains whitespace from gnomAD. Source gnomAD VCF already contains this, so I need to fix it at the Dockerfile.
Exception is as …