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While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance):

CLNSIG=2|2|2|2|2|2|2

This is actually reported in this example, so I think the usage of the pipe is quite common for genomic annotations of this kind.

Which is the use of the pipe (|) character? I looked for it in the VCF file format specification; however, only the meaning of the comma (,) is specified (i.e., presence of multiple alternate value for that field). I am wondering, instead, what the pipe represents.

Thank you.

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    $\begingroup$ There's some documentation on the GO annotation (GAF) format which goes on to define the pipe to mean 'OR'. I think this is somewhat supported by the NCBI gene annotation format for gene names e.g. BRCAI | BRCC1 | BROVCA1 | FANCS | IRIS | PNCA4 | PPP1R53 | PSCP | RNF53. But it may still be specific for VCF, so I will dig a little more but if nothing else this is my understanding. $\endgroup$ – CKM Apr 3 '17 at 15:06
  • $\begingroup$ This was my suspect, actually. I think that, e.g., an annotation string such as GENEINFO=BRCA1|BRCC1,BRCA1|FANCS could mean that the GENEINFO annotation can take two possible values, each one suggested by a different annotation source: 1) BRCA1|BRCC1: the first annotation source suggests that the variant is located either on BRCA1 or on BRCC1; 2) BRCA1|FANCS: the second annotation source suggests that the variant is located either on BRCA1 or on FANCS. I cannot find any documentation, though, so I am not sure this is the right interpretation. $\endgroup$ – Eleanore Apr 4 '17 at 5:57
  • $\begingroup$ Yet another question that could have fit in a bioinformatics stackexchange... $\endgroup$ – bli Apr 4 '17 at 7:37
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    $\begingroup$ @bli I completely agree with you. Unfortunately, Biology Stackexchange mixes biology and bioinformatics, and there is not a way of separating the two aspects. However, I agree that bioinformatics should have its own identity. $\endgroup$ – Eleanore Apr 4 '17 at 7:39
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    $\begingroup$ @bli biostars.org is so established at this point it diminishes the need for a bioinformatics SE other than having that integration with the other communities here (which would be nice, honestly). $\endgroup$ – CKM Apr 4 '17 at 14:20

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