SNPEff intragenic annotation

Question

[evcon]

I am using SNPEff to annotate variants called in dog canfam4. There are a lot of variants annotated as intragenic to GNG10. My understanding is that means they are variants outside of a transcript but still within a gene. The weird thing is those variants appear to be outside of the gene according to the GTF I used to build the reference. Here's an example variant marked as intragenic:

chr11   16418911    .   T   G   930.82  PASS    AC=4;AF=0.2;AN=20;BaseQRankSum=-2.048;DP=203;ExcessHet=4.5998;FS=5.995;InbreedingCoeff=-0.2515;MLEAC=4;MLEAF=0.2;MQ=60;MQRankSum=0;QD=11.78;ReadPosRankSum=-0.326;SOR=1.395;ANN=G|intragenic_variant|MODIFIER|GNG10|GNG10|gene_variant|GNG10|||n.16418911T>G||||||  

And here are all the lines in the GTF containing GNG10

chr11   refGene transcript  66634242    66640794    .   +   gene_id "GNG10"; transcript_id "NM_001205002";  gene_name "GNG10";

chr11   refGene exon    66634242    66634378    .   +   .   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "1"; exon_id "NM_001205002.1"; gene_name "GNG10";

chr11   refGene 5UTR    66634242    66634297    .   +   .   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "1"; exon_id "NM_001205002.1"; gene_name "GNG10";

chr11   refGene CDS 66634298    66634378    .   +   0   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "1"; exon_id "NM_001205002.1"; gene_name "GNG10";

chr11   refGene exon    66638937    66639068    .   +   .   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "2"; exon_id "NM_001205002.2"; gene_name "GNG10";

chr11   refGene CDS 66638937    66639059    .   +   0   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "2"; exon_id "NM_001205002.2"; gene_name "GNG10";

chr11   refGene 3UTR    66639063    66639068    .   +   .   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "2"; exon_id "NM_001205002.2"; gene_name "GNG10";

chr11   refGene exon    66639960    66640794    .   +   .   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "3"; exon_id "NM_001205002.3"; gene_name "GNG10";

chr11   refGene 3UTR    66639960    66640794    .   +   .   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "3"; exon_id "NM_001205002.3"; gene_name "GNG10";

chr11   refGene start_codon 66634298    66634300    .   +   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "1"; exon_id "NM_001205002.1"; gene_name "GNG10";

chr11   refGene stop_codon  66639060    66639062    .   +   gene_id "GNG10"; transcript_id "NM_001205002"; exon_number "2"; exon_id "NM_001205002.2"; gene_name "GNG10";

chr15   refGene transcript  8944034 8945119 .   -   .   gene_id "GNG10"; transcript_id "NM_001205002_2";  gene_name "GNG10";

chr15   refGene exon    8944034 8945119 .   -   .   gene_id "GNG10"; transcript_id "NM_001205002_2"; exon_number "1"; exon_id "NM_001205002_2.1"; gene_name "GNG10";

chr15   refGene 3UTR    8944034 8944874 .   -   .   gene_id "GNG10"; transcript_id "NM_001205002_2"; exon_number "1"; exon_id "NM_001205002_2.1"; gene_name "GNG10";

chr15   refGene CDS 8944878 8945081 .   -   0   gene_id "GNG10"; transcript_id "NM_001205002_2"; exon_number "1"; exon_id "NM_001205002_2.1"; gene_name "GNG10";

chr15   refGene 5UTR    8945082 8945119 .   -   .   gene_id "GNG10"; transcript_id "NM_001205002_2"; exon_number "1"; exon_id "NM_001205002_2.1"; gene_name "GNG10";

chr15   refGene start_codon 8945079 8945081 .   -   0   gene_id "GNG10"; transcript_id "NM_001205002_2"; exon_number "1"; exon_id "NM_001205002_2.1"; gene_name "GNG10";

chr15   refGene stop_codon  8944875 8944877 .   -   0   gene_id "GNG10"; transcript_id "NM_001205002_2"; exon_number "1"; exon_id "NM_001205002_2.1"; gene_name "GNG10";

What's going on here?

[Pierre Lindenbaum]

what was the command line for snpeff ?

[evcon]

My command was java -jar snpEff.jar eff \ canfam4 \ -noStats \ all.norm.filter.pval.vcf > all.norm.filter.pval.ann.vcf