Hi all,

Currently, I have been trying to annotate a mouse VCF file generated by Strelka using Annovar. I was able to download the gene annotations from UCSC using the following commands, and everything went fine until this step:

perl annotate_variation.pl -buildver mm10 -downdb -webfrom annovar refGene mouse_mm10/ perl annotate_variation.pl --buildver mm10 --downdb seq mouse_mm10/mm10_seq retrieve_seq_from_fasta.pl mouse_mm10/mm10_refGene.txt -seqdir mouse_mm10/mm10_seq -format refGene -outfile mouse_mm10/mm10_refGeneMrna.fa

When I tried to use table_annovar by running the following command, the job runs, but it generates an empty output.

table_annovar.pl/Users/caro mouse_mm10/ --vcfinput --outfile final --buildver mm10 --protocol refGene --operation g

Below is the message that is generated after I run the job. Would someone have any suggestions in what I am doing wrong here?

NOTICE: Running with system command <convert2annovar.pl -includeinfo="" -allsample="" -withfreq="" -format="" vcf4="" users="" carolinabatista="" desktop="" results_853="" strelka="" results="" passed.somaticteste.indels.vcf=""> final.avinput> NOTICE: Finished reading 1 lines from VCF file NOTICE: A total of 0 locus in VCF file passed QC threshold, representing 0 SNPs (0 transitions and 0 transversions) and 0 indels/substitutions NOTICE: Finished writing allele frequencies based on 0 SNP genotypes (0 transitions and 0 transversions) and 0 indels/substitutions for 0 samples NOTICE: Running with system command <table_annovar.pl final.avinput="" mouse_mm10="" -outfile="" final="" --buildver="" mm10="" --protocol="" refgene="" --operation="" g="" -otherinfo="" -nastring="" .="">

NOTICE: Processing operation=g protocol=refGene NOTICE: Running with system command <annotate_variation.pl -geneanno="" -buildver="" mm10="" -dbtype="" refgene="" -outfile="" final.refgene="" -exonsort="" final.avinput="" mouse_mm10=""/> NOTICE: Output files were written to final.refGene.variant_function, final.refGene.exonic_variant_function NOTICE: Reading gene annotation from mouse_mm10/mm10_refGene.txt ... Done with 36864 transcripts (including 5292 without coding sequence annotation) for 24540 unique genes

NOTICE: Multianno output file is written to final.mm10_multianno.txt NOTICE: Reading from final.mm10_multianno.txt

NOTICE: VCF output is written to final.mm10_multianno.vcf Use of uninitialized value $pre_anno_string in concatenation (.) or string at table_annovar.pl line 191, <manno> line 1. Use of uninitialized value in join or string at table_annovar.pl line 192, <manno> line 1. Use of uninitialized value in join or string at table_annovar.pl line 192, <manno> line 1. Use of uninitialized value in join or string at table_annovar.pl line 192, <manno> line 1. Use of uninitialized value in join or string at table_annovar.pl line 192, <manno> line 1. Use of uninitialized value in join or string at table_annovar.pl line 192, <manno> line 1. Use of uninitialized value in join or string at table_annovar.pl line 192, <manno> line 1. Use of uninitialized value in join or string at table_annovar.pl line 192, <manno> line 1.