I'd like to run Pindel on some WGS datasets (tumour and normal samples) mapped using BWA-MEM. According to the user guide, I can run option 1 after creating a bam-configuration file:
./pindel -f ref.fa -i 1222config.txt -c ALL -o sample_1222
However, this would compare all the samples to the reference genome, and not to each other (e.g. tumour vs somatic sample).
To directly compare two samples, my understanding is that I'd have to create a Pindel txt file from the bam files using Bam2Pindel. Is there any way I could compare two samples without processing them with Bam2Pindel first?