Came up with a paper on BMC genoics comparing five different somatic snp callers.

GATK UnifiedGenotyper in NaiveSubtract
MuTect1
SomaticSniper from the original paper
Installation help document for Strelka with updated user's guide and a quick start guide
And the original paper on somatic-sniper
VarScan2 from the original paper
Classical samtools method also works.

Calling variants with samtools/bcftools

Help from samtools protocol
Help from samtools/bcftools protocol