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Add an option to filter by position or for specific variants instead of gene name; check the reference allele for input variants.
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## Describe the issue
Hi, this is not a specific problem with VEP tool but more understanding issue.
I have a variant in PTEN with HGVSc: NM_000314.8:c.634+5G>C which annotated via VEP command line …
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Hi Alex,
I am trying to analyze allele-specific single cell RNAseq data collected through 10x chromium v2 and I was wondering if Wasp allele specific calling would work in the context of STAR solo.…
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Would it be possible to view th…
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## 1. Bug description
The FRQ and BETA is flipped as expected, but A1 and A2 keeps original
### Console output
******::NOTE::******
- Formatted results will be saved to `tempdir()` by defa…
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Hello Nicholas
Firstly thanks for developing this tool, it's really helpful!
Now I have Hi-C data from one individual, and I want to compare the contacts between two alleles (to see if allelic heter…
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Using the reads functionality it should be possible to provide the allele pileup for a specific position in the genome.
Looking at the distribution of alleles at a single genomic position is useful f…
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Hi there,
since GDC release 23 there is a new readout for TCGA, 'Allele-specific Copy Number Segment'. It would be great if it were downloadable in TCGAbiolinks via:
```R
query.cnv = TCGAbiolin…
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Hi Weilong,
I am trying to analyze allele specific methylation and while performing analysis using below parameter
$ cgmaptools asm -r refgenome.fa -b sample1_sorted.bam -l sample1_bayes.vcf -o s…
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Maybe do #758 first/same time
Anna B suggested:
* [Cancer hotspots](https://www.cancerhotspots.org/#/home)
* Onco KB (already there but not as quick links)
* Cancer bio (confirm link?)