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The fix to issue #1 has revealed another 'bug', this is to do with positions differing between genomic builds.
**Example**: after sorting chromosome 6 based on hg19 positions their are 639 varian…
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When running the pipeline, the generated report for some of the phenotypes does not always contain the QQ plot, instead showing:
**QQ Plot**
`Error in if (is.unsorted(-ypvs)) ypvs = sort.int(ypvs,…
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Hello,
Would it be possible to add an extra check for chr name in the gwas/TSV input not present in the genomic fasta and/or dbSNP file?
I am aware that this is handled by the alias file/switch, s…
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All the data for the R for genomics workshop is on a figshare instance with nice instructions.
https://figshare.com/articles/Data_Carpentry_Genomics_beta_2_0/7726454
From that we only need `combin…
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I already mentioned this in https://github.com/andersen-lab/ivar/issues/85#issuecomment-858686771, but I am opening its own issue because I think this is a separate problem.
There is an inconsisten…
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Hi,
I have tried re-generating the phaseI Ribo ORFs followed as the README indications, but no outputs were generated. Please tell me what's going on? Here are my command and its indications in the…
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**Is your feature request related to a problem? Please describe.**
We need consistent error codes for all errors and warnings so other tools can searh for them without error messages breaking flow.
…
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The DWG is seeking to line up with the HL7/FHIR specification for exchanging Ehealth records, and in particular, their Genomics component which provides a means of reporting variants with optional ass…
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For example, when "South America" is selected, it is clear that a numerical value is expected, but "South America = 0.00" is nonsensical unless you know the context/meaning of that label, which isn't …
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Currently hgvs objects are generated only on the basis of the parseability of the hgvs string. No variant validation is being done.
Expected result:
All hgvs variants should be consistent to a ref…