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Snipsift synonymous variant extraction

Hi everyone,

I want to filter synonymous variant from my vcf. What can I do?

I have used this command but I have seen that filtered file has also included synonymous variant;

java -jar SnpSift.jar filter "ANN[*].EFFECT != 'synonymous_variant'"

Thanks!

filtering snipsift
• 5,057 views • link
updated by Ram Ram • written by basalganglia • basalganglia

instead of =, try using has

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updated by Ram Ram • written by Deepak Tanwar Deepak Tanwar

I have tried that as

"ANN[*].EFFECT !has 'synonymous_variant'"
-bash: !has: event not found
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updated by Ram Ram • written by basalganglia • basalganglia

Is it like that "ANN[*].EFFECT !has "synonymous_variant""

It can not work

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updated by Ram Ram • written by basalganglia • basalganglia 
'ANN[*].EFFECT !has "synonymous_variant"'
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updated by Ram Ram • written by Deepak Tanwar Deepak Tanwar

Bash uses "!" expression in its history substitution command. So it confuses your command with history substitution function and throws an error that it didn't find such a command in its history.

Try temporarily turning off history substitution feature and turning it back on when you're done with your operations involving "!" :

set +H
<do your operations>
set -H
• 0 views • link
written by apuhegde • apuhegde

1 answer 

line 1:14 no viable alternative at input '[*].EFFECT!'
line 1:19 token recognition error at: '"'
java.lang.RuntimeException: java.lang.RuntimeException: LexerNoViableAltException('"')
        at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory.compile(LangFactory.java:128)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.parseExpression(SnpSiftCmdFilter.java:255)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:282)
        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)
Caused by: java.lang.RuntimeException: LexerNoViableAltException('"')
        at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory$1.recover(LangFactory.java:117)
        at org.antlr.v4.runtime.Lexer.nextToken(Lexer.java:169)
        at org.antlr.v4.runtime.BufferedTokenStream.fetch(BufferedTokenStream.java:187)
        at org.antlr.v4.runtime.BufferedTokenStream.sync(BufferedTokenStream.java:170)
        at org.antlr.v4.runtime.BufferedTokenStream.consume(BufferedTokenStream.java:154)
        at org.antlr.v4.runtime.Parser.consume(Parser.java:588)
        at org.antlr.v4.runtime.DefaultErrorStrategy.consumeUntil(DefaultErrorStrategy.java:758)
        at org.antlr.v4.runtime.DefaultErrorStrategy.recover(DefaultErrorStrategy.java:191)
        at ca.mcgill.mcb.pcingola.snpSift.antlr.SnpSiftParser.expression(SnpSiftParser.java:778)
        at ca.mcgill.mcb.pcingola.snpSift.antlr.SnpSiftParser.compilationUnit(SnpSiftParser.java:89)
        at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory.compile(LangFactory.java:125)
        ... 5 more
Caused by: LexerNoViableAltException('"')
        at org.antlr.v4.runtime.atn.LexerATNSimulator.failOrAccept(LexerATNSimulator.java:329)
        at org.antlr.v4.runtime.atn.LexerATNSimulator.execATN(LexerATNSimulator.java:250)
        at org.antlr.v4.runtime.atn.LexerATNSimulator.match(LexerATNSimulator.java:143)
        at org.antlr.v4.runtime.Lexer.nextToken(Lexer.java:165)
        ... 14 more

It can not work again :(

• 0 views • link
updated by Ram Ram • written by basalganglia • basalganglia

Just try "ANN[*].EFFECT ! 'synonymous_variant'"

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updated by Ram Ram • written by Deepak Tanwar Deepak Tanwar 
line 1:14 no viable alternative at input '[*].EFFECT!'

Ok, thanks. I have use = again

• 0 views • link
updated by Ram Ram • written by basalganglia • basalganglia

Hi basalganglia,

I'm having a similar problem (SNPSift - Token Recognition Error). I've tried the suggestions in this thread, but it hasn't worked for me. My error is a result of the "@" being in my ID name.

I was wondering if you could post your final command line so I could try to imitate it and see if it works for me? (I realize you've said "I have used "=" again", but I want to ensure I'm using the "=" correctly like you).

Cheers.

• 0 views • link
updated by Ram Ram • written by anon123 • anon123

Hi anon123,

"ANN[*].EFFECT != 'synonymous_variant'" is my command. But it is not work efficiently. Then I have translate my data to excel file then extract synonymous variants

• 0 views • link
updated by Ram Ram • written by basalganglia • basalganglia

Cheers, thanks for your help. :)

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written by anon123 • anon123

Check my reply to basalganglia.

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written by apuhegde • apuhegde

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