Pindel has an extremely large output

I am wondering if I am doing something wrong here.

I ran Pindel (alongside two other structural variant [SV] callers) on four WGS samples. The two other callers report approximately 50000 SVs and have a decent running time.

However, Pindel takes long to run and its output files are very large (VCF files of 9 GB, more than a million detected SVs). I never used Pindel before, but I am wondering if I am doing something wrong here.

My command to call Pindel (from Python to cmd) is:

pindel -f {} -i {} -o {} -T {}.format(reference, config_file, output_path, threads)


PS: I use Pindel version 0.2.5b9

I am mainly confused how Pindel reports so many more calls in comparison to the other two callers. I appreciate any suggestions or remarks!

• Some other SV callers have higher thresholds for SV sizes (I think Delly does not call anything small). If you would filter Pindel variants by the same treshold, would you get something comparable? Apr 28 '20 at 12:24
• I see. I could try to play around with the settings a little indeed. Thanks for the info! Apr 29 '20 at 15:01
• You could just check histograms of SV sizes, that would be probably the quickest way to figure if the difference has something to do with SV sizes (I am not sure, it was just a guess) Apr 29 '20 at 15:31