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When using RefSeq merged cache for GRCh37, VEP returns outdated symbols of some genes, even though the same genes are reported with the updatd symbol in RefSeq GFF.
For instance, genes IKBKAP and D…
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Dear,
I created the SNP index based on the vcf file of dbSNP156.
An error occurs when performing SNP comparison:
```mrsfast --search hg38.fa --seq ./test/rfx5.fa --threads 6 -e 100 --disable-sam-…
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Now that we've reconfigured and refactored the phasing pipeline to improve SV performance on 10Mbp, we probably need to make additional changes to improve scalability for whole chromosome/genome runs.…
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### Describe the bug
after syncing a newly created contact to my android phone, the phone numbers are missing.
### Steps to reproduce
* on a linux machine i create a new contact using khard. …
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Hi,
I am trying to run truvari on the hapdiff unphased variants VCF (produced by the haplotype resolved HG002 assemblies) against the HG002 benchmarking VCF. I have given the commands used and the …
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This recommendation was raised in the [review of the Poseidon paper](https://elifesciences.org/reviewed-preprints/98317v1/reviews#tab-content#tab-content).
> I could not find any discussion of refe…
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Use https://github.com/mskcc/variant-overlap or some other tool to add sample variant overlap metrics to the sample comparison workflows & output metrics, variants, and/or reports so that we can direc…
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To keep things flexible, I was thinking about using "source" or perhaps "grouping" as a name followed by two lists:
``` json
{
"sourceABC": {
"reference": ["sample1"],
"compariso…
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Is there a way to state what version of the reference genome a VCF file is using to make its comparison? Two questions:
1. Does this meta data exist in a VCF?
2. Is this something that Guacamole can s…
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Hello!
I have a question regarding the vcf that the **get** command outputs in comparison to the ***.txt***. I've noticed that I had two variants in the txt file both labelled as PASS but only one …