Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

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

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
5 changes: 5 additions & 0 deletions VCFv4.4.draft.tex
View file
Open in desktop
Original file line number Diff line number Diff line change
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}

Expand Down