SNPeff and SNPsift version incompatibility?

usegalaxy.eu support
1

I am running into an error trying to run SNPsift Extract fields after SNPeff and I think it’s because the versions currently available on usegalaxy.eu or use galaxy.org are possibly incompatible?

It seems SNPeff is v5.2 and SNPsift is v4.3. I therefore am getting parsing errors when using SNPsift, such as:

Exception in thread “main” java.lang.RuntimeException: Cannot parse EffectType ‘start_retained_variant’
at org.snpeff.snpEffect.EffectType.parse(EffectType.java:131)
at org.snpeff.vcf.VcfEffect.parseEffect(VcfEffect.java:888)
at org.snpeff.vcf.VcfEffect.parseAnn(VcfEffect.java:734)
at org.snpeff.vcf.VcfEffect.parse(VcfEffect.java:718)
at org.snpeff.vcf.VcfEffect.(VcfEffect.java:134)
at org.snpeff.vcf.VcfEntry.getVcfEffects(VcfEntry.java:756)
at org.snpsift.lang.expression.FieldEff.getFieldString(FieldEff.java:49)
at org.snpsift.lang.expression.Field.eval(Field.java:76)
at org.snpsift.SnpSiftCmdExtractFields.evaluate(SnpSiftCmdExtractFields.java:47)
at org.snpsift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:151)
at org.snpsift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:122)
at org.snpsift.SnpSift.run(SnpSift.java:588)
at org.snpsift.SnpSift.main(SnpSift.java:76)

If this is indeed the issue then is it possible that SNPsift can be updated (or access provided to SNPeff v4.3 in the tools)?

Thanks :slight_smile:

2

Hi,

Thanks for mentioning this. I am sorry for the inconvenience.

Do you know that you can change the version of a tool yourself? However, options are limited to a set versions that are installed on usegalaxy.*, which in this case includes V4.3.

You have to click on the versions button in the middle panel on top. This is an screenshot:

different_versions
different_versions1534×1086 350 KB

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3

Hi,
Thanks for that speedy reply - I had totally forgotten it is possible to select which version of the tool to use manually. Will try now!

:slight_smile:

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4

No problem at all. I hope it solves the problem.

5

It did solve the problem (matched version SnpEff to same version of SnpSift)

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