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Hello @jodyphelan,
We are currently implementing the analysis of IS6110 insertions onto our structural variants workflow, but we are running into some unexpected TBProfiler outputs.
The attache…
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For [this table](https://www.cbioportal.org/results/structuralVariants?cancer_study_list=msk_impact_2017&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2C…
inodb updated
1 month ago
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Hello,
I was running VEP (v105) on some CNV data and was wondering if it is meant to output HGVS notation for the CNVs or not?
The fields are empty so making sure I haven't run it wrongly or mi…
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Hi i am running mity via docker but encountered with some bam error, could not able to rectify it, actually i was trying to find out INDELS for long read ONT generated data, using minimap2 aligned bam…
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Sorry,
This is not a problem with your code rather my question
You have called structural variants with Crest and Delly and I called with Manta, how did you annotated the output of Crest or Del…
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### Description of the bug
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky)'
Caused by:
Process `NFCORE_RAREDISEASE:RARED…
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Hello, Ive been using the ngmlr v0.2.7 aligner along with Sniffles v2.2 on parasite genomes.
I generate a variant file but I am struggling to understand the difference between some of fields. For an…
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Hello,
Thanks for the package it is very useful and i was able to use it correctly but I haven’t included the use of structural variants (for plotting, since it is not used for calculations).
Could …
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http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/VCF%20(Variant%20Call%20Format)%20version%204.0/encoding-structural-variants
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Currently we assume that every variant is a focal change with a nucleotide `alt` sequence. This is only a subset of the VCF spec and doesn't allow us to load variants such as:
```
#CHROM POS ID RE…