VCFv4.3 - first batch of changes

Makefile

@@ -7,14 +7,16 @@ PDFS =	BCFv1_qref.pdf \
 	SAMv1.pdf \
 	tabix.pdf \
 	VCFv4.1.pdf \
-	VCFv4.2.pdf
+	VCFv4.2.pdf \
+	VCFv4.3.pdf
 
 pdf: $(PDFS)
 
 CRAMv2.1.pdf: CRAMv2.1.tex CRAMv2.1.ver
 SAMv1.pdf: SAMv1.tex SAMv1.ver
 VCFv4.1.pdf: VCFv4.1.tex VCFv4.1.ver
 VCFv4.2.pdf: VCFv4.2.tex VCFv4.2.ver
+VCFv4.3.pdf: VCFv4.3.tex VCFv4.3.ver
 
 
 .SUFFIXES: .tex .pdf .ver

VCFv4.1.tex

@@ -231,7 +231,7 @@ \section{Understanding the VCF format and the haplotype representation}
 \section{INFO keys used for structural variants}
 When the INFO keys reserved for encoding structural variants are used for imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g. SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each alelle (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles).
 
-The following INFO keys are reserved for encoding structural variants. In general, when these keys are used by imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g. SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each alelle (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles).
+The following INFO keys are reserved for encoding structural variants.
 \footnotesize
 \begin{verbatim}
 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
@@ -261,7 +261,7 @@ \section{INFO keys used for structural variants}
 ##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
 \end{verbatim}
 \normalsize
-For precise variants, the consensus sequence the alternate allele assembly is derivable from the REF and ALT fields. However, the alternate allele assembly file may contain additional information about the characteristics of the alt allele contigs.
+For precise variants, the consensus sequence of the alternate allele assembly is derivable from the REF and ALT fields. However, the alternate allele assembly file may contain additional information about the characteristics of the alt allele contigs.
 \footnotesize
 \begin{verbatim}
 ##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
@@ -498,7 +498,7 @@ \subsection{Encoding Structural Variants}
 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
 ##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
 #CHROM POS     ID        REF              ALT          QUAL FILTER INFO                                                               FORMAT       NA00001
-1      2827694 rs2376870 CGTGGATGCGGGGAC  C            .    PASS   SVTYPE=DEL;END=2827762;HOMLEN=1;HOMSEQ=G;SVLEN=-68                 GT:GQ        1/1:13.9
+1      2827694 rs2376870 CGTGGATGCGGGGAC  C            .    PASS   SVTYPE=DEL;END=2827708;HOMLEN=1;HOMSEQ=G;SVLEN=-14                 GT:GQ        1/1:13.9
 2       321682 .         T                <DEL>        6    PASS   SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62         GT:GQ        0/1:12
 2     14477084 .         C                <DEL:ME:ALU> 12   PASS   SVTYPE=DEL;END=14477381;SVLEN=-297;CIPOS=-22,18;CIEND=-12,32       GT:GQ        0/1:12
 3      9425916 .         C                <INS:ME:L1>  23   PASS   SVTYPE=INS;END=9425916;SVLEN=6027;CIPOS=-16,22                     GT:GQ        1/1:15

VCFv4.2.tex

@@ -515,7 +515,7 @@ \subsection{Encoding Structural Variants}
 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
 ##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
 #CHROM POS     ID        REF              ALT          QUAL FILTER INFO                                                               FORMAT       NA00001
-1      2827694 rs2376870 CGTGGATGCGGGGAC  C            .    PASS   SVTYPE=DEL;END=2827762;HOMLEN=1;HOMSEQ=G;SVLEN=-68                 GT:GQ        1/1:13.9
+1      2827694 rs2376870 CGTGGATGCGGGGAC  C            .    PASS   SVTYPE=DEL;END=2827708;HOMLEN=1;HOMSEQ=G;SVLEN=-14                 GT:GQ        1/1:13.9
 2       321682 .         T                <DEL>        6    PASS   SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62         GT:GQ        0/1:12
 2     14477084 .         C                <DEL:ME:ALU> 12   PASS   SVTYPE=DEL;END=14477381;SVLEN=-297;CIPOS=-22,18;CIEND=-12,32       GT:GQ        0/1:12
 3      9425916 .         C                <INS:ME:L1>  23   PASS   SVTYPE=INS;END=9425916;SVLEN=6027;CIPOS=-16,22                     GT:GQ        1/1:15
@@ -529,7 +529,7 @@ \subsection{Encoding Structural Variants}
 The example shows in order:
 \begin{enumerate}
   \item A precise deletion with known breakpoint, a one base micro-homology, and a sample that is homozygous for the deletion.
-  \item An imprecise deletion of approximately 105 bp.
+  \item An imprecise deletion of approximately 205 bp.
   \item An imprecise deletion of an ALU element relative to the reference.
   \item An imprecise insertion of an L1 element relative to the reference.
   \item An imprecise duplication of approximately 21Kb. The sample genotype is copy number 3 (one extra copy of the duplicated sequence).