Annotate VCF with SnpEff

[eweitz]

Take as input an unannotated VCF file, and output a VCF file with annotations.

@vlaufer, @erinkwagner, @HuaLing1, if you have time, please comment on which information that @cjav can expect in your output.

[ghost]

@erinkwagner @erinkwagner @cjav

all - here is what i will include:

annotate via GRCh38

java -Xmx4G -jar snpEff.jar -c ./snpEff.config -v GRCh38.p2.RefSeq test.chr22.vcf

From SNPEff website

####################Note:#####################

N.B. - By default the next step adds ALL database INFO fields.

add dbsnp stuff

java -jar SnpSift.jar annotate -dbsnp test.GRCh38.chr22.vcf > test.GRCh38.dbsnp.chr22.vcf

add clinvar annotations

java -jar SnpSift.jar annotate -clinvar test.GRCh38.dbsnp.chr22.vcf > test.GRCh38.dbsnp.clinvar.chr22.vcf

add dbnsfp stuff

java -jar SnpSift.jar dbnsfp -v -db ./data/dbNSFPv3.0a.txt.gz test.GRCh38.dbsnp.clinvar.chr22.vcf > test.GRCh38.clinvar.dbnsfp.chr22.vcf

the most thorough way to see what exactly this will add is by going on to our instance, and running these commands from /home/ubuntu/vlaufer/snpeff/snpEff

alternatively, /home/ubuntu/vlaufer/snpeff/snpEff/test.GRCh38.dbsnp.clinvar.chr22.vcf contains a vcf so annotated, but it does not yet have dbnsfp annotations, because those are in a database so large it is still downloading, so I cannot prototype that functionality yet (tomorrow AM).

The only other thing to incorporate is the GFF that carlos sent me - im looking at that now.

[erinkwagner]

Here are the snpEff annotation headings @cjav

Name Type

---

Allele string Annotation string Putative_impact string Gene_name_HGNC string Gene_ID string Feature_type string Feature_ID string Transcript_biotype string Rank_Total string HGVS.c string HGVS.p string cDNA_position string CDS_position string Protein_position string Distance_to_feature int Error_message string