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I'm attempting to implement Vardict as part of an analysis plan for the FDA's SEQ QC targeted sequencing work group. I'm getting an empty output from PE hybrid capture sequences when using VarDict-1.…
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Rationale: this allows to feed the variant data from PureCN into other programs like PyClone. Given CN segments with known allele CN one could always intersect the data between variants and CN segment…
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The function GeneratePonBedpe has parameter documentation
```
@Argument(shortName="NO", doc="VCF index of normal", optional=true)
public int NORMAL_ORDINAL = 1;
```
Since all of the inputs ar…
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This is not an issue but rather asking for advice.
I have two cohorts A and B. Variant calls from A and B are very different in terms of quality. I couldnt find anything on variant calling so i wan…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/185) by Fong Chun Chan (Bitbucket: [Fong Chun Chan](https://bitbucket.org/Fong Chun Chan), ).**
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Hi Sigve,
Wondering what was the rationale behind skipping variants which have "conflicting_interpretations_of_pathogenicity" by ClinVar regardless of other annotations that can be (likely) pathoge…
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>It is also important, in the introduction, and indeed for the presentation of information in the collated database, for the authors to be clear that the variant interpretation processes for germline …
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@davidbenjamin commented on [Fri Mar 03 2017](https://github.com/broadinstitute/gatk-protected/issues/927)
In tumor-only mode we can use correlations among variants to impute germline variants.
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I'm recently running PVACseq on a bunch of VEP-annotated germline variants vcf with netMHC, and some of the samples will show up an error of "Type names and field names must be valid identifiers" in C…
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Hi All,
We are trying to debug losing phased variants produced by mutect2 and vardict when we run the Callers in the order: [vardict, mutect2, gatk-haplotype].
Question 1 - phased variants
We a…