Annotate VCF on specific transcripts (ANN field)
1
0
Entering edit mode
3.5 years ago
FGV ▴ 170

Dear all,

I've been using snpEff and snpSift for a while to annotate and filter my VCF files. Usually I just annotate my VCF with snpEff but, as it is, snpEff annotates all transcripts. Recently I wanted to restrict my annotations (ANN) to a list of ~150 transcripts, but could not find a way to do it. Is it possible? As a workaround, I just re-annotated the VCF with snpEff the "-onlyTr" option, but it is annoying to have to annotate a VCF twice. Is there a way to just filter the annotations?

However, even with the "-onlyTr" option, I still get some annotations that should have been removed. In the example below, it annotates a variant on both MSH6 and FBXO11 genes, even though I only specified the transcript ENST00000234420. I guess it is because gene FBXO11 has no transcript, but if I am only interested on that list of transcripts, this gene should not be included, right?

thanks

2 48033890 . CT C 1846.7 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.216;ClippingRankSum=0.000;DP=498;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=4.44;ReadPosRankSum=-0.195;SOR=0.711;VQSLOD=4.16;culprit=SOR;ANN=C|intron_variant|MODIFIER|MSH6|ENSG00000116062|transcript|ENST00000234420|protein_coding|9/9|c.4002-10delT||||||INFO_REALIGN_3_PRIME,C|intragenic_variant|MODIFIER|FBXO11|ENSG00000138081|gene_variant|ENSG00000138081|||n.48033891delA|||||| GT:AD:DP:GQ:PL 0/1:254,162:416:99:1884,0,3658
vcf snpEff snpSift • 1.8k views
ADD COMMENT
0
Entering edit mode

Just a thought: maybe a custom GFF3 with just the gene/transcripts needed could be created and imported as a custom annotation database into snpEff. Then the annotation could be run against that database, which would probably save time, too.

ADD REPLY
0
Entering edit mode
3.5 years ago

I wrote a tool that removes the SNPEFF ANN annotation based on a list of gene-name/transcript http://lindenb.github.io/jvarkit/VcfBurdenFilterGenes.html

e.g:

 java -jar dist/vcfburdenfiltergenes.jar -a "NM_206933.2" in.vcf > out.vcf
ADD COMMENT

Login before adding your answer.

Traffic: 856 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6