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**Feature request description, and associated problem**
vv_hgvs is currently the main interface for VVTA databases and is used by VariantValidator for this purpose. Users expect to be able to query V…
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We need a enable the search of variants in the OpenTargets platform search.
## Background
It should be possible to search on
- variant id (chr_pos_ref_alt)
- search on exact ”chr_pos_” …
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As for other Statement types, we need to consider what constraints to put on the subject variation molecule type (genomic, transcript, protein) for Variant Pathogenicity statements. (e.g. for Molecul…
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Dear Developers,
We are trying to perform a BUSCO analysis in our assembly on a CentOS7 computer. While the Quast analysis is running successfully, we get 100% missing BUSCOs, even if we try the as…
ghost updated
3 years ago
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It seems mason_simulator crushes if there are >150 contigs in the fasta file.
mason_simulator -ir myfasta.fa -n 5000 -o left.fq -or right.fq
Error message:
MASON SIMULATOR
===============
…
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Dear @hemstrow
I was wondering if it would be easy to write a function to calculate dN/dS ration using snpEff annotated VCF file. Currently, there is no functional tool or package available to do …
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I am in a situation where I have a ClinVar VCF and I want to change all pathological variants in my BAM files into the REF (or N if possible) in order to not reveal any genomic vulnerabilities not rel…
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Hi,
I installed Variant Detective to work on bacterial genomes and found that Claire3 is not working - even with the test dataset.
Any idea what causes this behavior.
I have copied the log below fo…
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Hello,
I am relatively new in variant calling using scRNA-Seq. I have 17 datasets from 17 patients. I want to call the variants for each patient. I only need the list of variants in each sample.
Can…
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There is a difference in the result between refseq and ensembl and I'm not too sure why.
Basically when the genome build is GRCh38 and transcript_set is 'refseq', the variant `11-5248232-T-A` it s…