Using SnpEff to extract relevant fields

Question

[bishtamit078]

Hi all , I am new to SnpEff tool, i want to produce an annotated vcf file that contains relevant columns such as Gene, Transcript and Nucleotide Change and PopFreqMax. I think it is possible using SnpSift filters but don't know how to approach it, Is there any command or script... if yes plz comment.

Answer 1

[morovatunc]

If that measure is on the VCF header. We can do that. In order to filter some of the parameters you should first determine their measure in the vcf header. For example, in the snp+indel vcf, you may filter snp by basically saying cat vcf | java -jar $snpSiftjar filter "(exists SNP)"

[bishtamit078]

Thank you for the reply.. Here are steps what all i have done so far, please correct me where i am going wrong.

Step 1. Downloaded SnpEff zar file, Extracted into my home directory. Step 2. Downloaded GRCh37.75 from SnpEff official website and extract it into same location Step 3. Ran command java -Xmx4g -jar snpEff.jar -v -stats ex1.html GRCh37.75 example/file.vcf > eaxmples/file.ann.vcf Step 4. Got three files as output i.e. html,annotated and txt file.

Now i am trying to run the command you shared, but getting below error "Exception in thread "main" java.lang.RuntimeException: INFO field 'SNP' not found in VCF header"

Please let me know where I am going wrong..

Answer 2

[sbombin]

Hi, I had the same problem. Actually to filter your annotated VCF file based on impact like "High" impact for example, you need to run:

 java -jar SnpSift.jar filter "ANN[0].IMPACT has 'HIGH'" input_annot.vcf > output_annot_filtered.vcf