Hello,

I am trying to annotate SVs that I got by running NanoVar using Annovar (build hg38). Here are the commands I used to run Annovar.

annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/

annotate_variation.pl -buildver hg38 -downdb cytoBand humandb/

annotate_variation.pl -buildver hg38 -downdb -webfrom annovar exac03 humandb/ 

annotate_variation.pl -buildver hg38 -downdb -webfrom annovar avsnp147 humandb/ 

annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbnsfp30a humandb/

table_annovar.pl /scratch/pipe_try/nanovar/trimmed-hg38.pass.nanovar.vcf /scratch/RESOURCES/hg38/annovar_humandb -buildver hg38  -out /scratch/pipe_try/annotation/annotation.hg38.vcf -remove  -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a  -operation gx,r,f,f,f -nastring .  -vcfinput  -polish -xref gene_fullxref.txt

Although annotations from xref files are populating in the final annotated vcf, the ExacALL scores are just "." through out. Here is a sample of the vcf input (minus the headers) to Annovar:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  trimmed
chr1    350186  nv_SV18238-03RC4        N       <INV>   4.2     PASS   
SVTYPE=INV;END=248942250;SVLEN=248592064;SR=2;NN=0.622  GT:DP:AD        1/1:2:0,2
chr1    475602  nv_SV10120-J3V6N        N       ]chr1:710590]N  2.6     PASS    
SVTYPE=BND;END=.;SVLEN=.;SR=2;NN=0.448;SV2=TLO  GT:DP:AD        0/1:4:2,2
chr1    710580  nv_SV11577-6U3XJ        N       <INS>   6.9     PASS    
SVTYPE=INS;END=710581;SVLEN=285;SR=3;NN=0.796   GT:DP:AD        1/1:3:0,3
chr1    710590  nv_SV10120-J3V6N        N       N[chr1:475602[  2.6     PASS    
SVTYPE=BND;END=.;SVLEN=.;SR=2;NN=0.448;SV2=TLO  GT:DP:AD        0/1:4:2,2
chr1    908929  nv_SV18386-NW18S        N       <DEL>   4.4     PASS    
SVTYPE=DEL;END=909323;SVLEN=-393;SR=2;NN=0.639  GT:DP:AD        1/1:2:0,2
chr1    1993702 nv_SV20252-FSNKQ        N       <DUP>   2.7     PASS    
SVTYPE=DUP;END=1993884;SVLEN=182;SR=2;NN=0.462  GT:DP:AD        1/1:2:0,2
chr1    3016310 nv_SV8827-Q7X8T N       <DUP>   4.4     PASS    
SVTYPE=DUP;END=3016710;SVLEN=400;SR=2;NN=0.637  GT:DP:AD        1/1:2:0,2
chr1    3016310 nv_SV8828-UPN0K N       <INS>   3.7     PASS    
SVTYPE=INS;END=3016311;SVLEN=606;SR=2;NN=0.572  GT:DP:AD        0/1:3:1,2
chr1    3501983 nv_SV10305-3X4TN        N       <DUP>   4.0     PASS    
SVTYPE=DUP;END=3502114;SVLEN=131;SR=2;NN=0.601  GT:DP:AD        1/1:2:0,2

Here is a portion of the output generated by Annovar:

1       475602  nv_SV10120-J3V6N        N       ]1:710590]N     2.6     PASS    SVTYPE=BND;END=.;SVLEN=.;SR=2;NN=0.448;SV2=TLO;ANNOVAR_DATE=2018-04-16;Func.refGene=intergenic;Gene.refGene=OR4F3\x3bLOC100132287;GeneDetail.refGene=dist\x3d23924\x3bdist\x3d15154;ExonicFunc.refGene=.;AAChange.refGene=.;pLi.refGene=.;pRec.refGene=.;pNull.refGene=.;Gene_full_name.refGene=.;Function_description.refGene=.;Disease_description.refGene=.;Tissue_specificity(Uniprot).refGene=.;Expression(egenetics).refGene=.;Expression(GNF/Atlas).refGene=.;P(HI).refGene=.;P(rec).refGene=.;RVIS.refGene=.;RVIS_percentile.refGene=.;GDI.refGene=.;GDI-Phred.refGene=.;cytoBand=1p36.33;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;avsnp147=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;ALLELE_END  GT:DP:AD        0/1:4:2,2
 1       3501983 nv_SV10305-3X4TN        N       <DUP>   4.0     PASS    SVTYPE=DUP;END=3502114;SVLEN=131;SR=2;NN=0.601;ANNOVAR_DATE=2018-04-16;Func.refGene=intronic;Gene.refGene=MEGF6;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;pLi.refGene=4.42421031130217e-15;pRec.refGene=0.994620434269407;pNull.refGene=0.00537956573058837;Gene_full_name.refGene=multiple_EGF_like_domains_6;Function_description.refGene=.;Disease_description.refGene=.;Tissue_specificity(Uniprot).refGene=.;Expression(egenetics).refGene=unclassifiable_(Anatomical_System)\x3bmyocardium\x3bheart\x3bovary\x3burinary\x3bcolon\x3bparathyroid\x3bfovea_centralis\x3bchoroid\x3blens\x3bskin\x3bretina\x3bprostate\x3boptic_nerve\x3blung\x3bplacenta\x3bmacula_lutea\x3btestis\x3bkidney\x3bbrain\x3b;Expression(GNF/Atlas).refGene=.;P(HI).refGene=0.11042;P(rec).refGene=0.09881;RVIS.refGene=2.072624965;RVIS_percentile.refGene=97.81198396;GDI.refGene=6730.46373;GDI-Phred.refGene=17.39874;cytoBand=1p36.32;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;avsnp147=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;ALLELE_END      GT:DP:AD        1/1:2:0,2

I am wondering why the ExacALL scores do not populate at all. Is there some sort of preprocessing that is required before Annovar is run on NanoVar generated VCF file? Secondly, I noticed NanoVar like other callers such as Sniffles do not give nucleotides for REF and ALT columns instead they those columns substituted by N and <sv_type>. Does this hinder Annovar from annotating properly?

Thank you, Asma