Here the VCF 4.5 spec says there are 5 possible top-level types you "must" use for the ID of an ##ALT header line:
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The first level type must be one of the following: |
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\begin{itemize} |
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\item DEL Region of lowered copy number relative to the reference, or a deletion breakpoint |
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\item INS Insertion of novel sequence relative to the reference |
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\item DUP Region of elevated copy number relative to the reference, or a tandem duplication breakpoint |
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\item INV Inversion of reference sequence |
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\item CNV Region of uniform copy number (may be deletion, duplication or copy number neutral) |
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\end{itemize} |
None of those is R or M. But then in the next section it has an example using those, for IUPAC codes:
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Symbolic alleles can be used also to represent genuinely ambiguous data in VCF, for example: |
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\begin{verbatim} |
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##ALT=<ID=R,Description="IUPAC code R = A/G"> |
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##ALT=<ID=M,Description="IUPAC code M = A/C"> |
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\end{verbatim} |
So are only those 5 possible top-level types plus IUPAC codes allowed?
Here the VCF 4.5 spec says there are 5 possible top-level types you "must" use for the
IDof an##ALTheader line:hts-specs/VCFv4.5.tex
Lines 259 to 266 in c101c79
None of those is
RorM. But then in the next section it has an example using those, for IUPAC codes:hts-specs/VCFv4.5.tex
Lines 285 to 289 in c101c79
So are only those 5 possible top-level types plus IUPAC codes allowed?