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The [current gist](https://gist.github.com/ckandoth/f265ea7c59a880e28b1e533a6e935697) to download the ExAC VCF and whitelist known somatic events, will also inadvertently whitelist indels that overlap…
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Following on from https://github.com/umccr-illumina/dragen/issues/53
vc-enable-phasing is currently running by default in the somatic pipeline and generating FORMAT/PS tags
To enable combing SNVs …
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There are hard treshholds in the scripts that filters false positive somatic SNVs/indels. These pertain to the read depth, allele counts and fraction as well as gnomAD population frequencies and PoN c…
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HI ,
PHMM can not work in somatic variants calling ?
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Clinical Significance - current clinical significance does not adequately support the needs for somatic variant information.
- Current set of values defined by LOINC
![image](https://github.com/Co…
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Thanks a lot for this great tool. I have some puzzles wanting for help
1 Can it be used for somatic
2 can it call EGFR or other genes complex variants
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e.g. there was an issue with some oncogenic TP53 variants being filtered because they also occurred in germline
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Hi Ryan,
I've read your posts on using SVTyper to help with somatic variant filtering. You suggested only keeping variants that have a non-reference genotype in the tumor (GT != 0/0) and variants t…
mej54 updated
6 years ago
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### Description of the bug
As you mention in your Nextflow pipeline: @https://nf-co.re/sarek/3.0.2/parameters it would be possible to obtain the results of tumor-only somatic variant calling using st…
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Hello,
The outputs from running ClairS on PacBio (hifi_revio platform) are providing less than 5 somatic SNVs. We identified multiple high-confidence somatic variants from short-read sequencing on s…