Question: filter non synonymous using SnpSift
gravatar for zion22
16 months ago by
zion2240 wrote:

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


snp sequence software error • 634 views
ADD COMMENTlink modified 16 months ago by SMK1.9k • written 16 months ago by zion2240
gravatar for SMK
16 months ago by
SMK1.9k wrote:

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
ADD COMMENTlink modified 16 months ago • written 16 months ago by SMK1.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 492 users visited in the last hour