However, I noticed that the latest version of Pindel (0.2.5b1) has the --NormalSamples option. According to the usage prompt, this flag turns on germline variant filtering:
Turn on germline filtering, less sensistive and you may miss somatic calls (default false)
I run Pindel as follows:
pindel -f hg19.fa -i bam_config_file.txt -o Test1 --NormalSamples
My bam configuration file looks like:
/path/to/tumor/bam insert_size Tumor
/path/to/normal/bam insert_size Normal
However, I noticed that the output still contains germline indels. So perhaps the --NormalSamples hasn't been fully implemented yet and I'll still need to post-process results to get somatic indels from Pindel?