Abstract 5108: A combined processing and assessment workflow for SNV and indel calling on exome sequencing of tumor samples

Abstract

Abstract A workflow for exome sequencing is established using multiple callers for SNV and indel. A spectrum of measures is looked at to understand the diversity and characteristics of the samples. Two common workflows for variant calling are used, namely GATK unified genotyper and Samtools mpileup. Illumina paired end 90 base reads are mapped to the human genome using BWA. Variants called by GATK and Samtools are compared and merged to give a unified set of calling in VCF format. This approach gives additional confidence in calls supported by both callers as there are technical differences in the two workflows. dbSNP rate and TI/TV ratio are used to assess the general quality (sensitivity and specificity) of the calls. It is observed that tumor samples with very low and high TI/TV novel ratio are largely lung and melanoma samples respectively. They are likely to be UV and smoking induced DNA mutation. This affects the overall TI/TV ratio. A handful of samples also exhibit high variant count that is uniquely found (private) in the sample alone. This correlates with lower than expected dbSNP rate. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5108. doi:1538-7445.AM2012-5108