VCFv4.5 RC2 #770
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VCFv4.5 RC2 #770
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Changed PDFs as of 2b64c97: VCFv4.5.draft (diff). |
d-cameron
commented
May 29, 2024
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- Do we need better support for use cases such as subsetting a 5mC assay to just CpG methylation. Do we need to support (optional) caching of sequence context.
-- The current model requires a reference genome to know context. - Do we need a header/tag to explicitly state stranded/unstranded CpG
VCFv4.5.draft.tex
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| M5hmC & . & Float & Alias for M76792 5-(hydroxymethyl)cytosine \\ | ||
| M6mA & . & Float & Alias for M28871 6-methyladenine \\ | ||
| M[0-9]+[ACGTUN] & M & Float & Fraction of bases modified with the given ChEBI ID. \\ | ||
| DPM[0-9]+[ACGTUN] & M & Float & Total read depth for reads able to detect the base modification with the given ChEBI ID. \\ |
VCFv4.5.draft.tex
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| M6mA & . & Float & Alias for M28871 6-methyladenine \\ | ||
| M[0-9]+[ACGTUN] & M & Float & Fraction of bases modified with the given ChEBI ID. \\ | ||
| DPM[0-9]+[ACGTUN] & M & Float & Total read depth for reads able to detect the base modification with the given ChEBI ID. \\ | ||
| ADM[0-9]+[ACGTUN] & M & Float & Read depth for reads with the base modification with the given ChEBI ID. \\ |
VCFv4.5.draft.tex
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| @@ -637,70 +714,42 @@ \subsubsection{Genotype fields} | |||
| \item LPL: is a list of $n \choose \mathrm{Ploidy}$ integers giving phred-scaled genotype likelihoods (rounded to the closest integer; as per PL) for all possible genotypes given the set of alleles defined in the LAA local alleles. | |||
| The precise ordering is defined in the GL paragraph. | |||
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| \item M[0-9]+ (Float): DNA or RNA base modification abundance for the modification with the given ChEBI ID. | |||
| \item M[0-9]+[ACGTN] (Float): Fraction of DNA or RNA bases modified with the given ChEBI ID. | |||
| @@ -196,8 +196,56 @@ \subsubsection{Individual format field format} | |||
| \item LR: Identical to R except the only alternate alleles defined in the $LAA$ field are considered present. | |||
| \item LG: Identical to G except the only alternate alleles defined in the $LAA$ field are considered present. | |||
| \item P: The field has one value for each allele value defined in $GT$. | |||
| \item M: The field has one value for each possible base modification for the corresponding ChEBI ID. | |||
| \end{itemize} | |||
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Add gVCF expansion
| \vspace{0.5em} | ||
| \begin{tabular}{ l l l l l l l l l l} | ||
| \#CHROM & POS & REF & ALT & FORMAT & SAMPLE\\ | ||
| chr & $10$ & C & A & GT:M5mC & \tt{0/1:0.95}\\ |
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Just reading this record, it is unknown whether these values are for all 5mC, just CpG methylation, and whether it is stranded or not.
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Arbitrary co-methylation is out of scope but do we want special fields for CpG co-methylation? |
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Changed PDFs as of f1e0634: VCFv4.5.draft (diff). |
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VCF 4.5 Release Candidate 2 changes:
MMtag abbreviations