Need some clarifications in snpEFF annotation in extracting exonic variants

Question

[bioinforesearchquestions]

Hi All,

I have generated single vcf for 2 samples. Then annotated the vcf file using snpEff and I extracted only variants for gene "GLA".

In my case for the below two variants, there are more than one annotation. Multiple annotations are separated by comma.

1) Why am I getting multiple annotation for one variant?

I am interested in extracting only exonic variants. Mutations in exon regions will affect the protein by either creating missense and nonsense mutations. As per the below summary, I have variants from exon "73,274". I believe, non_coding_exon_variant and non_coding_transcript_variants are also included in 73,274.

Why the non_coding variants are clubbed with exons?

Answer 1

[Raony Guimarães]

1) Why am I getting multiple annotation for one variant?

Because one position can map to multiple features and genes at the same time. If you want only one annotation per variant you have to use the option:

-canon : Only use canonical transcripts.

Why the non_coding variants are clubbed with exons?

Same reason of first question, to avoid this you can use the option:

-onlyProtein : Only use protein coding transcripts. Default: false

[bioinforesearchquestions]

Dear Raony,

In snpEff command , when I gave

case1:

java -Xmx12G -jar snpEff.jar eff -c snpEff.config -v -i vcf -o vcf -onlyProtein true hg19 Fam_15_35_VC.160522.recal.filtered.vcf > Fam_15_35_VC.160522.recal.filtered.snpEff.onlyprot.vcf 2>log_onlyprotein.txt

I am getting the following error:

Error : Unknown parameter 'Fam_15_35_VC.160522.recal.filtered.vcf'

Command line : SnpEff -i vcf -o vcf true hg19 Fam_15_35_VC.160522.recal.filtered.vcf

If you see the command line from the error, there is no "-onlyProtein", but the true value is present.

Then I tried following case by removing "true" and just gave -onlyProtein:

Command: java -Xmx12G -jar snpEff.jar eff -c snpEff.config -v -i vcf -o vcf -onlyProtein hg19 Fam_15_35_VC.160522.recal.filtered.vcf > Fam_15_35_VC.160522.recal.filtered.snpEff.onlyprot.vcf 2>log_onlyprotein.txt

It worked. But "-onlyProtein, Default is false"