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The VICC gene fusions project, in partnership with representatives from ClinGen Somatic, CGC, and the CAP/ACMG Cytogenomics Committee, has developed a draft specification for the representation of gen…
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Hi
I'm performing the TWAS analysis using weights of GTEx(version 8).
The following datasets are based on hg19:
1. The LD reference data (https://data.broadinstitute.org/alkesgroup/FUSION/LDREF.t…
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Hello,
At UMCCR, we use arriba as a fusion caller for WTS clinical samples for cancer patients. Arriba is part of our WTS production pipeline setup and works great.
We have recently encountered …
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Hi all,
We had a FISH positive sample with SS18 fusion.
We did a target capture for ~100 target genes including SS18. Due to the low quality of the sample, the RIN of the sample is quite low, le…
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Our current reliance on INTEGRATE (for fusion detection) and INTEGRATE-NEO for annotation of the fusion junction peptide is problematic.
It would be desirable if we could support fusion calls from …
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Hi, @nadiadavidson or other developers!
Thanks for making JAFFA available for long sequencing reads, which I believe is very urgent for the identification of fusion transcripts using widely applied…
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I am working on D.Melanogaster
I want to make a custom blaclist.
I have three control biological replicate.
Do you have a recommended way to build a blaclist from those control?
I did not find i…
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I allowed myself to create a new issue since mine and Yulong don't seem to have the same answers after all. So, the two lines I respectively used to run braker1 and braker2 are :
braker.pl --genome=…
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I am having some trouble parsing annotation, gff3 file and peptide file. This worked with the example data, but not my own data. Would appreciate tips on how to parse these files properly. Files, code…
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_tl;dr
The current variant index has several shortcomings that affect our production infrastructure, our ability to update it to a newer GnomAD version and our ability to consider rare variants withi…