Here are a few more, a summary of the other answers, and updated links:
- BAYSIC (paper) - method for combining sets of genome variants
- CAKE (abstract, paper) - pipeline that combines four other variant callers
- deepSNV (abstract, paper)
- EBCall (abstract, paper)
- GATK SomaticIndelDetector (note: only available after an annoying sign-up and login)
- Indelocator
- Isaac variant caller (abstract, paper)
- joint-snv-mix (abstract, paper)
- LoFreq (abstract, paper) (call on tumor & normal separately and then use a filter to derive somatic events)
- MutationSeq (abstract, paper)
- MutTect (abstract, paper) (note: only available after an annoying sign-up and login)
- Pindel
- QuadGT (for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents)
- samtools mpileup - by piping BCF format output from this to bcftools view and using the '-T pair' option
- Seurat (abstract, paper)
- Shimmer (abstract, paper)
- SolSNP (call on tumor & normal separately and then compare to identify somatic events)
- SNVMix (abstract, paper)
- SOAPsnv
- SomaticCall (manual)
- SomaticSniper (abstract, paper)
- Strelka (abstract, paper)
- VarDict
- VarScan2 (abstract, paper)
- Virmid (abstract, paper)
For a much more general discussion of variant calling (not necessarily somatic or limited to SNVs/InDels) check out this thread: What methods do you use for In/Del/SNP calling?
Some papers describing comparisons of these callers:
- Comparing somatic mutation-callers: Beyond Venn diagrams.
- A comparative analysis of algorithms for somatic SNV detection in cancer
- Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers
- Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.
The ICGC-TCGA DREAM Mutation Calling challenge has a component on somatic SNV calling.
This paper used validation data to compare popular somatic SNV callers:
Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers
You can also use freebayes to call them. Specify --pooled-discrete and --genotype-qualities, call germline/somatic at the same time, and then pass the result through vcfsamplediff (vcflib).
Virmid paper has been published in Genome Biology. Please enjoy. http://genomebiology.com/2013/14/8/R90/abstract
Note: Please read PDF version instead of the html full text. The publication team made a mistake to replace two figures with another :( It will be fixed soon anyway.
Can Virmid call InDels? When I use Virmid, it only give me SNPs. And I didn't see any parameters that can allow me to call InDels.
You'll need to update the link to MuTect. Broad Institute has begun to put portable versions of their tools on Github, like the latest release of MuTect. The Genome Institute at WashU has been using Github for a while, but portable versions of their tools can be found here and here.