filter non synonymous using SnpSift

Question

[zion22]

Hi. Thank for reading this I have a problem, when i used the next command from SnpSift software:

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

The program didn't filter it as I wish. because when I compared 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 even I did it with others10 vcf files and I have the same problem. pd: my_original_file.vcf come from SnpEff

thanks

Answer 1

[AK]

When you generated the vcf files using SnpEff, did you add -formatEff? In the newer version of SnpEff, 'EFF' field is replaced by 'ANN' field unless you add -formatEff (Important changes: 'ANN' field). So if you didn't add -formatEff, you can try this one:

java -jar SnpSift.jar filter "ANN[*].EFFECT has 'missense_variant'" -f my_original_file.vcf