-
Hi Jeremiah,
I am trying to convert svaba output to a BEDPE format (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format), to adapt it for SV signature analysis as done…
-
### Need
As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in highly filtered T+N c…
-
- [ ] For each assay-type supported by Roslin, extract normal sample genotype columns from unfiltered VCFs, and merge into massive multi-sample VCFs per assay-type - listing all events observed in nor…
-
In attempting to use SURVIVOR_ant, we encountered segfaults when using VCFs from DELLY, Breakseq or MetaSV. The manta VCF files appear to be handled correctly.
The command below will segfault:
su…
-
#if $interval_file
cat ./strelkaAnalysis/chromosomes/\$int/somatic.snvs.vcf | grep -v "^#.*" >> $snvs;
cat ./strelkaAnalysis/chromosomes/\$int/somatic.indels.vcf | grep -v "^#.*" >…
-
Interested if people thinks this makes sense, and how much work it would entail.
For the pt189 analysis, I'd like to view pileups for an arbitrary set of BAMs (normal exome, plus multiple somatic exo…
-
[Svim](https://github.com/eldariont/svim) and [sniffles](https://github.com/fritzsedlazeck/Sniffles) are two SV callers specifically for long-read sequence data. It would be highly beneficial to be ab…
-
Hi guys,
I get regular requests from collaborators to look if we have seen germline variants in a specific gene within our AFHCS or GA cohorts. I've created a 'Gene Search' analysis to have a quick…
-
Hello,
When I run strelka2 somatic variants calling with "--reportEVSFeatures", I got variants vcfs containing values of "TumorSampleAltAlleleFraction". Those values are very close to "Somatic all…
-
**Describe the bug**
VarDict SVs once again end up in the SNV VCF files, making them hard to visualise for the user when loaded in Scout.
**To Reproduce**
Load e.g. case `novelbear` (or presumabl…
dnil updated
7 months ago