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Introduction: Next Generation Sequencing (NGS) is cost-effective, capable to investigate the genes faster but the protocol has challenges throughout its steps. Objective: We investigated different adjustments of protocol to screen the BRCA genes using Ion Torrent PGM sequencing and correlate the results with number of False Positive (FP) variants. Material and methods: Library preparation process, number of FP InDels, library concentration, number of cycles in amplify targets step, purity of nucleic acid, input, and number of samples/Ion 314 chip were analyzed in association with the results obtained by NGS. Results: 51 reactions and 9 adjustments of protocols were done and 8 FP InDels were observed in homopolymer regions. No FP Single-Nucleotide Polymorphism variant was observed. Protocol variables jointly are associated in 67.5% with the quality of results obtained(p<0.05). The number of FP InDels decreased when the quality of results increased. Conclusion: Ion AmpliSeq BRCA1/BRCA2 Community Panel had better performance with 4 samples per Ion-314 chip instead of 8 and the number of cycles in the amplification step, even using DNA with high quality, was better with 23. We observed better results when the manual equalization process was done, without the Ion Library Equalizer kit. These adjustments provided higher coverage of the variants and fewer artifacts (6.7-fold). Laboratories must perform the internal validation because FP InDel variants can vary according to the quality of results. NGS assay must be validated with Sanger.