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!