Hello, never used annovar. Did you check the documentation, they have nice tutorials there. To select deletions, you can use bcftools : bcftools view -i 'ILEN<0' <input.vcf>

@bestone, You can try ensembl vep or snpEff for the annotation of you vcf files and keep the output format as tab delimited file, doing this would be easier for futher variant filtering and interpretation steps. Hope this helps.