snpeff

[mmmm]

I have determined the snps (after mapping to the reference) and got vcf4 file with snps position within the chromosome
then I used snpEff to look at the effect of these snps BUT which output file includes the position of the snp and its effect (as in the snpeff.txt- only the effect of snps is listed within the gene but it does not refere to the snp position)??

[blakeoft]

You should get a new vcf file as output. It should have all of the info of the original vcf, plus some new information in the INFO field following this format

EFF= Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_Length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )

See http://snpeff.sourceforge.net/SnpEff_manual.html#output for more details.

EDIT: According to the same page, it looks like you need to redirect the output. Their example:

# Go to the directory where snpEff is installed
cd snpEff

# Do this only if you don't already have the database installed.
java -jar snpEff.jar download -v GRCh37.66

# Annotate the file
java -Xmx4g -jar snpEff.jar eff -v GRCh37.66 file.vcf > file.eff.vcf

[mmmm]

yes- thanks
I have got this, so this snp is synonomas in coding region but which gene/ region??- and what other information to be extracted?

DP=18;VDB=1.751185e-01;AF1=1;AC1=2;DP4=0,0,7,11;MQ=60;FQ=-81;EFF=DOWNSTREAM(MODIFIER||4283||257|yaaA||CODING|NP_459010.1||1),DOWNSTREAM(MODIFIER||576||21|thrL||CODING|NP_459006.1||1),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V165|820|thrA||CODING|NP_459007.1|1|1),UPSTREAM(MODIFIER||1970||309|thrB||CODING|NP_459008.1||1),UPSTREAM(MODIFIER||2903||428|thrC||CODING|NP_459009.1||1)

[blakeoft]

It looks like snpEff has reported five different effects that this SNP could have. The gene names are in the sixth field inside each parentheses. They are yaaA, thrL, thrA, thrB, and thrC. The specific location of the variant should be in second column of the record. What you have posted is only the seventh (INFO) column.

Look back at http://snpeff.sourceforge.net/SnpEff_manual.html#output for more information about what snpEff adds to the INFO column.