I'm getting "Segmentation fault (core dumped)" error when running Pindel on bam files from Ion Torrent. I only need to run for chromosome 13 but tried running for ALL chromosomes as well, without success. Yesterday, I've tested Pindel on bam files from Illumina and had no problems. I'm using Pindel 0.2.5b8, 20151210.
I've tried ../pindel -f chr13.fa C04config.txt -c 13:28,608,00-28,608,600 -o C04output.
Are bam files from Ion Torrent incompatible with Pindel? Any suggestions or advice would be greatly appreciated.