How to use snpEff filter for getting particluar column in annotated file

Question

[bishtamit078]

I am trying to add column such as Transcript, Nucleotide Change and PopFreqMax in my output annotated file. Here are the Steps that i have performed.

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.

After successfully completing these steps i got an annotated file, but it does not have any of the field mention above. I also tried "cat cancer.vcf | java -jar SnpSift.jar filter "(exists SNP)"" but got error "Exception in thread "main" java.lang.RuntimeException: INFO field 'SNP' not found in VCF header".

Any command or script that i need to run ?

please help me out in solving this problem.

Answer 1

[Medhat]

This fields "Transcript, Nucleotide Change and PopFreqMax" not added by snpEff.

Only these fields under ANN:

ALLELE (alias GENOTYPE) EFFECT (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.) IMPACT: { HIGH, MODERATE, LOW, MODIFIER } etc...

For more please see the documentation http://snpeff.sourceforge.net/SnpEff_manual.html#input

There is No filed called SNP in the header so you can not use

java -jar SnpSift.jar filter "(exists SNP)""