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vcf: VCF 4.5 gVCF example has off-by-one errors #781

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zaeleus opened this issue Aug 8, 2024 · 0 comments
Open

vcf: VCF 4.5 gVCF example has off-by-one errors #781

zaeleus opened this issue Aug 8, 2024 · 0 comments
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@zaeleus
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zaeleus commented Aug 8, 2024

In The Variant Call Format Specification: VCFv4.5 and BCFv2.2 (2024-06-28) § 5.5 "Representing unspecified alleles and REF-only blocks (gVCF)", some of the records in the example have FORMAT LEN values that are off-by-one.

diff --git a/VCFv4.5.tex b/VCFv4.5.tex
index e288aa9..00e4e7b 100644
--- a/VCFv4.5.tex
+++ b/VCFv4.5.tex
@@ -1862,12 +1862,12 @@ An example with both FORMAT LEN and a redundant INFO END is given below:
 \begin{tabular}{ l l l l l l l l l l }
 \#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & Sample \\
 1 & 4370 & . & G & $<$*$>$ & . & . & END=4383 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:25:60:23:0,60,900;14 \\
-1 & 4384 & . & C & $<$*$>$ & . & . & END=4388 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:25:45:25:0,42,630;4 \\
+1 & 4384 & . & C & $<$*$>$ & . & . & END=4388 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:25:45:25:0,42,630;5 \\
 1 & 4389 & . & T & TC,$<$*$>$ & 213.73 & . & . & GT:DP:GQ:PL:LEN & 0/1:23:99:51,0,36,93,92,86 \\
 1 & 4390 & . & C & $<$*$>$ & . & . & END=4390 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:26:0:26:0,0,315;1 \\
-1 & 4391 & . & C & $<$*$>$ & . & . & END=4395 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:27:63:27:0,63,945;4 \\
+1 & 4391 & . & C & $<$*$>$ & . & . & END=4395 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:27:63:27:0,63,945;5 \\
 1 & 4396 & . & G & C,$<$*$>$ & 0 & . & . & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:24:52:0,52,95,66,95,97 \\
-1 & 4397 & . & T & $<$*$>$ & . & . & END=4416 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:22:14:22:0,15,593;19 \\
+1 & 4397 & . & T & $<$*$>$ & . & . & END=4416 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:22:14:22:0,15,593;20 \\
 \end{tabular}
 \end{flushleft}
 \normalsize
@jmarshall jmarshall added the vcf label Aug 8, 2024
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