extract polyformisms non synonymous using SnpSift

Question

[zion22]

Hi, sorry to bother you. I ask in this forum why maybe someone can help me, some of you know how I could extract polyformisms non synonymous using SnpSift? and if you have an example of the command I appreciated it very much. Thank you

Answer 1

[Arup Ghosh]

The SnpSift filter option can be used to extract variants based on annotation and other parameters.

java -jar SnpSift.jar filter "( EFF[0].EFFECT = 'NON_SYNONYMOUS_CODING' )"  annotated.vcf > non_syn.vcf

Ref: http://snpeff.sourceforge.net/SnpSift.html#filter

[zion22]

Hi. Thank you so much for helping me. but I have a problem, when I run the next command:

java -jar SnpSift.jar filter "( EFF[0].EFFECT = 'NON_SYNONYMOUS_CODING' )"  my_original_file.vcf > NON_SYNONYMOUS_file.vcf

when I compare the two files, original and filtered, are exactly the same, even when I change the filter parameter NON_SYNYMOUS_CODING to SYNONYMOUS_CODING the output file is the same. if you know what I could do it would be great since I have to do it with 10 other vcf files and I have the same problem

[Arup Ghosh]

Can you share a snippet of the vcf file including the header?