I have been using ANNOVAR for a while with my tumor samples. I do not have control rarther am trying to understand the variants that are novel for my samples not present in dbSNP and are common in tumor and its corresponding IPS lines. I have extracted the non synonymous SNPs for my samples after annotation and prioritized the candidates on the basis of the functional scores reported by the annovar in its output file but when I am trying to understand the processing for the INDELS, am not getting any scores reported in the ANNOVAR output. The manual filtering I did for my INDELS using GATK was ( --filterExpression "QD < 2.0 || ReadPosRankSum < -20.0 || FS > 200.0" --filterName GATKStandard --missingValuesInExpressionsShouldEvaluateAsFailing ). Now I used this vcf file which I get from this step to annotate using ANNOVAR but in the exome_summary.csv of the ANNOVAR output I do not see any functional scores at all. Is there any way to prioritize the candidates? Or I should just take into account the large INDELS based on the quality score? Any method of prioritizing the INDEL ANNOVAR output without functional scores that can be suggested? I will be more interested in frameshift INDELS but how will I asses the impact on the protein functions from the annovar output if there is no functional scores to suggest how much damaging they are. Then there are a lot of genes where I can see INDELS but they are marked as unknown which means they have never been annotated but then how shall I use them or prioritize from them as well? Is there any strategy that can be applied?