Question: SnpSift filtering with missense variant error command
0
gravatar for basalganglia
4.2 years ago by
basalganglia30
England
basalganglia30 wrote:

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

missense error snipsift • 1.4k views
ADD COMMENTlink written 4.2 years ago by basalganglia30

Hi Basalganglia,

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

ADD REPLYlink written 2.8 years ago by bioinforesearchquestions210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1269 users visited in the last hour