SnpSift filtering with missense variant error command

Question

[basalganglia]

Hi everyone,

I want to filter missense variant form my vcf file with following command,

java -jar SnpSift.jar filter "(ANN[*].EFFECT = 'missense_variant')" a.vcf > b.vcf

I got this response,

Exception in thread "main" java.lang.RuntimeException: Cannot parse EffectType '5_prime_UTR_truncation+exon_loss_variant'
        at ca.mcgill.mcb.pcingola.snpEffect.EffectType.parse(EffectType.java:88)
        at ca.mcgill.mcb.pcingola.vcf.VcfEffect.parseEffect(VcfEffect.java:845)
        at ca.mcgill.mcb.pcingola.vcf.VcfEffect.parseAnn(VcfEffect.java:701)
        at ca.mcgill.mcb.pcingola.vcf.VcfEffect.parse(VcfEffect.java:685)
        at ca.mcgill.mcb.pcingola.vcf.VcfEffect.<init>(VcfEffect.java:227)
        at ca.mcgill.mcb.pcingola.vcf.VcfEntry.parseEffects(VcfEntry.java:926)
        at ca.mcgill.mcb.pcingola.snpSift.lang.expression.FieldEff.getFieldString(FieldEff.java:60)
        at ca.mcgill.mcb.pcingola.snpSift.lang.expression.Field.eval(Field.java:60)
        at ca.mcgill.mcb.pcingola.snpSift.lang.expression.ExpressionBinary.eval(ExpressionBinary.java:25)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.evaluate(SnpSiftCmdFilter.java:140)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:298)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:268)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:360)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:69)

What should I do?

Thanks

[bioinforesearchquestions]

Hi Basalganglia,

I am also getting the same error, did you get a chance to resolve this issue?