Entering edit mode
2.3 years ago
evcon
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10
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?
what was the command line for snpeff ?
My command was java -jar snpEff.jar eff \ canfam4 \ -noStats \ all.norm.filter.pval.vcf > all.norm.filter.pval.ann.vcf