MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics
Fig 2
Venn diagrams of called SNVs in MutAid by four variant callers with BWA, Bowtie2 and GSNAP mapping (A) Freebayes (B) GATK-HaplotypeCaller. (C) SAMTOOLS and (D) VarScan2.
GATK shows 93.29% overlap between at least two mappers whereas Varscan2 shows least overlap among all four variant callers with 78%. SAMTOOLS and Freebayes show 92.23% and 88%, respectively, agreement with at least two mappers.