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Most variant callers work by promiscuously outputting potential variants using a statistical model and then aggressively filtering down those variants with a series of filters. It would be useful to e…
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Hi, we have noted that assemblies generated with Flye very frequently introduce variants that are not supported by the reads, particularly at highly repetitive regions (but also in others as well). On…
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### Need
The number of SVs uploaded to Scout for WGS cases in balsamic is much higher than is common, and could really benefit from being reduced. As an example here are the some values from the mo…
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I have those two variants in my vtools variant database:
```
4 106156653 T C Scan1,Scan2 ....,.,.,.,....
4 …
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Use case: variant callers that insert fixed sample names like VarScan, or the TCGA data, which uses NORMAL/TUMOR as sample names.
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GDC: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
- features we'd like to support: snv, indel, structural variants, extra chromosomal dna
- create ta…
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Hi Dear Kosugi,
When I analyse output files I see that caller.TF file has true positive INS type variants but caller.eval file shows lines in below:
INS
2 3 4 5 6 7 8 9 10 12
…
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Hello,
I'm looking for a way to merge my SNP calls from different callers, and identify and SNPs identified from at least 2 of 3 callers to give me more confidence in my results.
I haven't yet f…
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Sorry to bother you again, after using the ONT data to call the structure variation, we modified the VCF content with format_add_ALTseq_LR.R. The following error occurred, so we checked the VCF file, …
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Hello Brad,
I have a question/request about the output from running ensemble variant caller, specifially the format field. At the moment the ensemble vcf file reports the format field from the first …