I was using Pindel-0.2.5 (latest version) on SUSE Linux to process a single bam file but getting a segmentation fault. I tried adjusting the window size (-w) to minimum, setting the -l false and -k false but it didn't seem to work. Anyone have any ideas on this?
can you post the last 50 lines of your console output (or send an email to email@example.com) and show me where it went wrong? provide your ref.fa.fai and samtools view -H output. I might need a small part of your bam to produce the error, if we cannot find the reason based on the console output, the reference, bam index files. BTW, can you tell me your command line as well? is this 0.2.5 specific? do you have the same issue with earlier version?