Gasp, a non-proportional Venn diagram ;o
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WouterDeCoster
BWA and samtools and bcftools for exome sequencing?
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To have better results I think you need to do the recalibration step.
as shown here http://www.htslib.org/workflow/
More:
Systematic comparison of variant calling pipelines using gold standard personal exome variants
Detailed comparison of two popular variant calling packages for exome and targeted exon studies
Validation and assessment of variant calling pipelines for next-generation sequencing
Yes, but being non-proportional you could as well put it in a table and be as clear as this venn diagram.
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WouterDeCoster
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Depends on how you've used these programs. Can you post some commands, particularly at the variant calling step?
From my experience, SAMtools/BCFtools is better for calling Sanger-confirmed SNVs than GATK, but not indels.