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Hi Joelle,
I hope you're well. I'd be very grateful if you could please help me with a confusing issue in burden testing where variants from certain gene sets are:
- present in the same chromosome…
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So far, all of the disease mappings to single diseases represent 'causal' relation.
i.e. a gene has been functionally linked to the disease phenotypes.
I also have examples I have noted where a …
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Repeat expansion variants were first introduced before v1.0, in #94. Back then they were using a separate ClinVar TSV dump. The next improvement will arrive in the upcoming v2.0 release and will use t…
tskir updated
3 years ago
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As we are introducing variant and study entities (and potentially locusToGene), metadata for them no longer should be stored in the evidence object. However other fields like l2g and credible sets are…
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Hiya,
Can Arriba be used to detect fusions in single-cell RNAseq data (e.g. Smart-seq2). I expect to see a greater number of false positives compared to bulk RNAseq, and with a lower number of read…
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Since dbSNP vcf is huge (15G) from https://ftp.ncbi.nih.gov/snp/latest_release/VCF/ .
I want to use slivar to annotate `RS`
```
##INFO=
```
use origin file `GCF_000001405.25.gz`, I got error mess…
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Hi!
I am testing out the updates in 2.1.0 and came across a behaviour I hadn't seen in the previous versions of cpsr.
With 2.1.0 (incl. the latest reference bundle), the attached input, and the…
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I have several done files (in alphabetical order: fastqs, remapping, retagging, variants, and vartrix) so think I'm stuck at the clustering stage (also as clusters_tmp.tsv is 0 bytes)
```
the web …
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Thank you for an excellent and well-documented resource.
According to the catalogue
"Before insertion into GenPhenSQL, all variant coordinates were normalized with bcftools norm; variants that
…
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Dear Mike,
I am wondering How LD clumping was performed to select eQTLs for candidate gene in eQTL-based two-sample Mendelian Randomization? How to handle pleiotropy eQTL issue? for example, a SNP …