Snpeff Error: No White-Space, Semi-Colons, Or Equals-Signs Are Permitted In Info Field.

Question

[William]

When trying to annotatie SNPs (produced by GATK ) I get a lot of error messages from snpEff.

Example:

Error while processing VCF entry (line 1676) : 10 11338256 . T G 10.3 LowQD;LowQual;StrandBias;VeryLowQual ABHom=0.40;AC=2;AF=1.00;AN=2;BaseQRankSum=1.231;DP=8;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=35.5726;MQ=21.44;MQ0=0;MQRankSum=0.358;OND=0.75;QD=1.29;ReadPosRankSum=-1.231;SB=19.11 GT:AD:DP:GQ:PL 1/1:3,2:8:3.01:39,3,0 java.lang.RuntimeException: No white-space, semi-colons, or equals-signs are permitted in INFO field. Value:"DOWNSTREAM(MODIFIER||||cops4|proteincoding|CODING|ENSDART00000064215|),UTR3PRIME(MODIFIER||||PLAC8 (2 of 2)|proteincoding|CODING|ENSDART00000145346|)"

The strange thing is that equal sign and semi colons look like their are part of the vcf format: http://www.1000genomes.org/node/101

Does this error message make sense to anyone?

[jackuser1979]

Have you able to figure out whats causing error? Did you fixed it? Bcos, I am also encountring the same problem. Your solution will be helpful to me.

[William]

No I switched to the stand alone tool from Ensembl Variant Effect Prediction: http://www.ensembl.org/info/docs/variation/vep/index.html

Answer 1

[utillich]

This bug was fixed in snpEff 3.1 revision H.

I had the same error, emailed a bug report to the developer, and he had it fixed and uploaded in less than an hour! If you are still affected with the newest version, I suggest you also submit a bug report.

Answer 2

[Raony Guimarães]

which version of snpeff are you using ?

To annotate a vcf using snpeff you basically have to do:

java -Xmx4G -jar snpEff.jar eff -v -onlyCoding true -i vcf -o vcf GRCh37.64 your.vcf > snpEff_output.vcf

so you will get a field like this on INFO

EFF=Effect1(EffectImpact|EffectFunctionalClass|CodonChange|AminoAcidChange|GeneName|GeneBioType|Coding|TranscriptID|ExonID),Effect2(etc...

and them you run

java -jar dist/GenomeAnalysisTK.jar \ -T VariantAnnotator \ -R /humgen/1kg/reference/humang1kv37.fasta \ -A SnpEff \
--variant 1000G.exomes.vcf \ (file to annotate) --snpEffFile snpEff_output.vcf \ (SnpEff VCF output file generated by running SnpEff on the file to annotate) -L 1000G.exomes.vcf \ -o out.vcf

to get a VCF like this:

1 874779 . C T 279.94 . AC=1;AF=0.0032;AN=310;BaseQRankSum=-1.800;DP=3371;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4493;InbreedingCoeff=-0.0045; MQ=54.49;MQ0=10;MQRankSum=0.982;QD=13.33;ReadPosRankSum=-0.060;SB=-120.09;SNPEFFAMINOACIDCHANGE=G215;SNPEFFCODONCHANGE=ggC/ggT; SNPEFFEFFECT=SYNONYMOUSCODING;SNPEFFEXONID=exon1874655874840;SNPEFFFUNCTIONALCLASS=SILENT;SNPEFFGENEBIOTYPE=proteincoding;SNPEFFGENENAME=SAMD11;SNPEFFIMPACT=LOW;SNPEFFTRANSCRIPTID=ENST00000342066

Source: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Genomic_Annotations_Using_SnpEff_and_VariantAnnotator

[William]

I use version 21b . The command I run is

java -Xmx4G -jar snpEff.jar eff -i vcf -o vcf Zv9.66 /data/wim/Analysis/Smart-mix-16-05-12116/DS.SNV.all2filtered.vcf 1> snpEff1.vcf 2>snpEff2.vcf