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PSL example fix and index base clarification #828

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d-cameron merged 1 commit into from
Sep 9, 2025
Merged

PSL example fix and index base clarification #828

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12 changes: 6 additions & 6 deletions VCFv4.4.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -598,7 +598,7 @@ \subsubsection{Genotype fields}
\item PSL (List of Strings): The list of phase sets, one for each allele specified in the {\tt GT}.
Unphased alleles (without a $\mid$ separator before them) must have the value '$.$' in their corresponding position in the list.
Unlike {\tt PS} (which is defined per CHROM), records with different CHROM but the same phase-set name are considered part of the same phase set.
If an implementation cannot guarantee uniqueness of phase-set names across the VCF (for example, phasing a streaming VCF or each CHROM is processed independently in parallel), new phase-set names should be of the format CHROM*POS*ALLELE-NUMBER of the ``first'' allele which is included in this set, with ALLELE-NUMBER being the index of the allele in the {\tt GT} field, since multiple distinct phase-sets could start at the same position. \footnote{The `*' character is used as a separator since `:' is not reserved in the CHROM column.}
If an implementation cannot guarantee uniqueness of phase-set names across the VCF (for example, phasing a streaming VCF or each CHROM is processed independently in parallel), new phase-set names should be of the format CHROM*POS*ALLELE-NUMBER of the ``first'' allele which is included in this set, with ALLELE-NUMBER being the one-based index of the allele in the {\tt GT} field, since multiple distinct phase-sets could start at the same position. \footnote{The `*' character is used as a separator since `:' is not reserved in the CHROM column.}
A given sample-genotype must not have values for both PS and PSL.
In addition, PS and PSL are not interoperable, in that a PS mentioned in one variant cannot be referenced in a PSL in another, since when used in PS it isn't connected to any specific haplotype (i.e. first or second), but PSL is.

Expand All @@ -607,8 +607,8 @@ \subsubsection{Genotype fields}
\vspace{0.5em}
\begin{tabular}{ l l l l l l l l l l}
\#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & SAMPLE1\\
chr19 & $5$ & . & T & G & . & PASS & DP=100 &GT:PSL & \tt{|0/1:chr9*5*1,.}\\
chr20 & $10$ & . & A & T,G & . & PASS & DP=100 &GT:PSL & \tt{|1/2|3:chr20*10*1,.,chr9*5*1} \\
chr19 & $5$ & . & T & G & . & PASS & DP=100 &GT:PSL & \tt{|0/1:chr19*5*1,.}\\
chr20 & $10$ & . & A & T,G & . & PASS & DP=100 &GT:PSL & \tt{|1/2|3:chr20*10*1,.,chr19*5*1} \\
chr20 & $15$ & . & G & C & . & PASS & DP=100 &GT:PSL & \tt{1|2:.,chr20*10*1}\\
\end{tabular}

Expand All @@ -624,9 +624,9 @@ \subsubsection{Genotype fields}
\vspace{0.5em}
\begin{tabular}{ l l l l l l l l l l}
\#CHROM & POS & REF & ALT & INFO & FORMAT & SAMPLE1\\
chr1 & $10$ & T & $<$DUP$>$ & SVCLAIM=DJ & GT:PSL:PSO & \tt{/0/0|1:.,.,chr1*10*1:.,.,3}\\
chr1 & $20$ & A & G & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*1:.,.,4,1} \\
chr1 & $30$ & G & T & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*1:.,.,2,5} \\
chr1 & $10$ & T & $<$DUP$>$ & SVCLAIM=DJ & GT:PSL:PSO & \tt{/0/0|1:.,.,chr1*10*3:.,.,3}\\
chr1 & $20$ & A & G & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*3:.,.,4,1} \\
chr1 & $30$ & G & T & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*3:.,.,2,5} \\
\end{tabular}

Without defining PSO, it would be ambiguous as to which copy of the duplicated region the SNVs occur on.
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12 changes: 6 additions & 6 deletions VCFv4.5.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -771,7 +771,7 @@ \subsubsection{Genotype fields}
\item PSL (List of Strings): The list of phase sets, one for each allele value specified in the {\tt GT}.
Unphased alleles (without a $\mid$ separator before them) must have the value '$.$' in their corresponding position in the list.
Unlike {\tt PS} (which is defined per CHROM), records with different CHROM but the same phase-set name are considered part of the same phase set.
If an implementation cannot guarantee uniqueness of phase-set names across the VCF (for example, phasing a streaming VCF or each CHROM is processed independently in parallel), new phase-set names should be of the format CHROM*POS*ALLELE-NUMBER of the ``first'' allele which is included in this set, with ALLELE-NUMBER being the index of the allele in the {\tt GT} field, since multiple distinct phase-sets could start at the same position. \footnote{The `*' character is used as a separator since `:' is not reserved in the CHROM column.}
If an implementation cannot guarantee uniqueness of phase-set names across the VCF (for example, phasing a streaming VCF or each CHROM is processed independently in parallel), new phase-set names should be of the format CHROM*POS*ALLELE-NUMBER of the ``first'' allele which is included in this set, with ALLELE-NUMBER being the one-based index of the allele in the {\tt GT} field, since multiple distinct phase-sets could start at the same position. \footnote{The `*' character is used as a separator since `:' is not reserved in the CHROM column.}
A given sample-genotype must not have values for both PS and PSL.
In addition, PS and PSL are not interoperable, in that a PS mentioned in one variant cannot be referenced in a PSL in another, since when used in PS it isn't connected to any specific haplotype (i.e. first or second), but PSL is.

Expand All @@ -780,8 +780,8 @@ \subsubsection{Genotype fields}
\vspace{0.5em}
\begin{tabular}{ l l l l l l l l l l}
\#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & SAMPLE1\\
chr19 & $5$ & . & T & G & . & PASS & DP=100 &GT:PSL & \tt{|0/1:chr9*5*1,.}\\
chr20 & $10$ & . & A & T,G & . & PASS & DP=100 &GT:PSL & \tt{|1/2|3:chr20*10*1,.,chr9*5*1} \\
chr19 & $5$ & . & T & G & . & PASS & DP=100 &GT:PSL & \tt{|0/1:chr19*5*1,.}\\
chr20 & $10$ & . & A & T,G & . & PASS & DP=100 &GT:PSL & \tt{|1/2|3:chr20*10*1,.,chr19*5*1} \\
chr20 & $15$ & . & G & C & . & PASS & DP=100 &GT:PSL & \tt{1|2:.,chr20*10*1}\\
\end{tabular}

Expand All @@ -797,9 +797,9 @@ \subsubsection{Genotype fields}
\vspace{0.5em}
\begin{tabular}{ l l l l l l l l l l}
\#CHROM & POS & REF & ALT & INFO & FORMAT & SAMPLE1\\
chr1 & $10$ & T & $<$DUP$>$ & SVCLAIM=DJ & GT:PSL:PSO & \tt{/0/0|1:.,.,chr1*10*1:.,.,3}\\
chr1 & $20$ & A & G & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*1:.,.,4,1} \\
chr1 & $30$ & G & T & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*1:.,.,2,5} \\
chr1 & $10$ & T & $<$DUP$>$ & SVCLAIM=DJ & GT:PSL:PSO & \tt{/0/0|1:.,.,chr1*10*3:.,.,3}\\
chr1 & $20$ & A & G & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*3:.,.,4,1} \\
chr1 & $30$ & G & T & . & GT:PSL:PSO & \tt{/0/0|0|1:.,.,chr1*10*1,chr1*10*3:.,.,2,5} \\
\end{tabular}

Without defining PSO, it would be ambiguous as to which copy of the duplicated region the SNVs occur on.
Expand Down