Pindel -x option

Question

[znl207]

I want to find out if it is possible to filter the size of structural variants using the -x options.

In the Pindel documentation -x indicates the maximum size of structural variations to be detected (1=128, 2=512, 3=2,048, 4=8,092, 5=32,368, 6=129,472, 7=517,888, 8=2,071,552)

Say I wanted only variants greater than 1000bp? Does anyone know if there is a way to do this? Thanks

Answer 1

[goodez]

-n/--min_NT_size                 only report inserted (NT) sequences in deletions greater than this size (default 50)
-v/--min_inversion_size          only report inversions greater than this number of bases (default 50)

[znl207]

Hi, Your response doesn't address the question of setting min / max for identifying insertions, deletions, and duplications. (-n is inserted seq in deletions not the deletion as a whole.) It seems like this is simply not an option in pindel.

[goodez]

Or just filter the results after running pindel.