Hi everyone, I am performing NGS data analysis for the discovery of somatic variants in target sequencing experiment, I used Ion Torrent data and made the variant calling with two different tools (Vardict and Mutect2). I have chosen two open source instruments because I do not have the proprietary TVC software, I have obtained very discordant results. Few variants in common, Mutect2 also detected more variants. Could someone tell me why so much discord?
Thanks in advance.
With so many parameter configurations for these programs, and also while considering the differences in sequencing depth and error rates of reads coming from different instruments and library preparation kits, benchmarking is difficult. One would probably require a discussion by the developers of these programs in order to begin to elucidate why they disagree on some calls.