Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
I'm wondering about the time Pindel takes on our machine for a whole genome analysis. When I run Pindel for a 90x-coverage file and use 22 Cores, it takes about 4 days to completion. I'm aware that it has to take longer for higher coverage, but this seems a bit unreasonable compared to the 4.5 hours runtime which is mentioned in the initial Pindel paper. Further I have not seen that any other people had an issue with the runtime.
The command I'm using is:
Hi!
I'm wondering about the time Pindel takes on our machine for a whole genome analysis. When I run Pindel for a 90x-coverage file and use 22 Cores, it takes about 4 days to completion. I'm aware that it has to take longer for higher coverage, but this seems a bit unreasonable compared to the 4.5 hours runtime which is mentioned in the initial Pindel paper. Further I have not seen that any other people had an issue with the runtime. The command I'm using is:
./pindel -f ref_file.fa -i configfile -T 22 -o outputIn the configfile is only one BAM file mentioned. Do you have any idea why its taking so long? Do you have suggestions how to improve the runtime?
I would greatly appreciate your help!
Thanks, David