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document convention for "QC squeezing" in population VCF #527

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document convention for "QC squeezing" in population VCF #527

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5 changes: 5 additions & 0 deletions VCFv4.4.draft.tex
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Expand Up @@ -1409,6 +1409,11 @@ \subsection{Representing unspecified alleles and REF-only blocks (gVCF)}
\end{flushleft}
\normalsize

\subsection{Selective genotype fields in many-sample VCF}
In VCF data representing SNPs and small indels jointly discovered and genotyped across a population, typically the vast majority of genotype fields are homozygous for the reference allele (0/0). When these GT entries are accompanied by the full array of quality-control FORMAT fields supporting variant genotypes (e.g. AD, SB, PL), the resulting file size may grow disproportionately to the practical utility of these fields.

To ameliorate this, joint variant calling tools may opt to order FORMAT fields so that most of them can be omitted in most entries (invoking the previous clause, ``Trailing [FORMAT] fields can be dropped, with the exception of the GT field''). For example, the FORMAT fields might be ordered {\tt GT:DP:AD:SB:PL} so that entries lacking significant evidence of variation may write GT and DP only (e.g. {\tt 0/0:32}). DP might furthermore be binned in some way, to improve compressibility. Tools consuming many-sample VCF files should accommodate this convention.

\pagebreak
\section{BCF specification}

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