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.

@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