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I'm munging a bunch of OpenGWAS data with MSS, and i noticed that the number of variants dropped due to being non-biallelic was quite high (hundreds of thousands-millions). In some cases, up to half t…
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## Need
We should improve the filtering strategy for SVs, ideally with soft-filtering whenever possible.
We have many open issues regarding this. We should add these changes or close these issues…
fevac updated
9 months ago
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References to sequences via GA4GH `SQ.` identifiers has been a feature of VRS since 1.0. However, these digests (based on the RefGet spec) do not contain information about the sequence alphabet or the…
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Comment from Katherine on genetic variation methods: Did you filter the SNPs by missing data or minor allele frequency prior to comparisons? If so, provide those values here, even if they are a defaul…
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- Input will be the files in the “ready to harmonise” directory - a wathcPath channel factory might be suitable for this
- The final harmonised files will also be sorted by genomic location, bgzipped…
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**Describe the bug**
An anonymous user has been trying to validate the `NM_000109.2:r.4540G>C` but this triggers an ERROR message to the sysadmins.
On screen, the error message is `Unable to valid…
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Dear all. I am new to deepvariant. We are trying to use deepvariant on a HPC cluster with singularity.
We installed nvidia and cuda drivers through conda, and tested it with other python programs tha…
melop updated
7 months ago
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I just created this issue to discuss fusion nomenclature proposed by M Li.
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All integers in Fortran are signed. It is a common request to include unsigned integers. At the very least to help with the interoperation with the C API that uses unsigned integers.
The best appro…
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### Is your feature related to a problem?
There are no mitochondrial variants reported in the output SNP file
### Describe the solution you'd like
It looks like the haplotagged.bam doesn't output r…