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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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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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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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The current behavior of ```bcf_update_info``` in vcf.c is to use the END info tag to set rlen
This field should instead be computed for symbolic variants (eg ``````)
My interpretation of the spe…
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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…
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When listing genes included in structural variants what is the order the genes are listed? would it be possible to keep the genomic order instead? this will be much more useful specifically to be able…