Sentence examples for mutation calls were from inspiring English sources

The mutation calls were annotated by ANNOVAR [ 13].

Mutation calls were determined using a MassARRAY Typer 4.0 Analyzer, according to the manufacturer's specifications.

Mutation calls were performed using Mutect and GATK software (Broad Institute, Cambridge, MA).

The cobas EGFR test results were considered invalid if any or all of the mutation calls were reported as invalid.

The binary mutation calls were derived from exome-sequencing data (all non-silent mutations) and copy number variation data (focal amplifications and deletions).

Discordant mutation calls were an EGFR S725I mutation (patient 8) and ABL1 G250E mutation (patient 18) detected by Sequenom but not by MiSeq, and a BRAF V600E mutation (patient 20) detected by MiSeq but not by Sequenom.

We found that the OncoMap platform achieved nearly 100% specificity in both fresh/frozen and FFPE-derived tumor DNA, indicating that false positive mutation calls are likely to be relatively rare with this approach.

A limitation of all methods investigated stems from our assumption that the somatic mutation calls are complete and accurate.

The majority of false positive mutation calls are generated from mismapped reads, for example, paralogs were mistakenly mapped to a single locus.

However, these false mutation calls are consistent across samples (Additional file 1: Figure S1) and thus the false mutation proportion of each mutation type can be estimated individually at each nucleotide position.

The human reference genomes GRCh37, GRCh37-lite, and HG19 used for mutation calling were downloaded according to the CGHub websites' 'Reference Assemblies' guideline (available at https://browser.cghub.ucsc.edu/help/assemblies).