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Sample ID and filter update #414

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Sample ID and filter update #414

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yfarjoun
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@jmarshall jmarshall added the vcf label Jun 13, 2019
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Modify FILTER header line to add optional Target=<SUBSET of Variant,Genotype, and Sample>

Required for Sample filters.

@yfarjoun yfarjoun marked this pull request as ready for review July 24, 2019 21:00
@yfarjoun yfarjoun changed the title draft of sample ID and filter update Sample ID and filter update Jul 24, 2019
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Changed PDFs as of ae2612a: VCFv4.2 (diff), VCFv4.3 (diff).

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Changed PDFs as of 6369341: VCFv4.2 (diff), VCFv4.3 (diff).

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Changed PDFs as of aaadf53: VCFv4.2 (diff), VCFv4.3 (diff).

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See also htsget PR #430 which ran into some difficulty over the question of whether commas may appear in sample names.

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yfarjoun commented Nov 3, 2019

should this modify 4.2 or only 4.3?

In the \verb!SAMPLE! line:
\begin{itemize}
\item{ID} is a string that identifies the sample.
It comprises non-whitespace characters and doesn't include the comma (`.') character.
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Comma in the parentheses 😄

@@ -240,6 +240,13 @@ \subsubsection{Sample field format}
##SAMPLE=<ID=Sample2,Assay=Exome,Ethnicity=CEU,Disease=Cancer,Tissue=Breast,Description="European patient exome from breast cancer">
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need to add FILTER to the line itself.

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