Question: Pindel -x option
0
gravatar for znl207
4 months ago by
znl20710
znl20710 wrote:

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

ADD COMMENTlink modified 4 months ago by goodez460 • written 4 months ago by znl20710
0
gravatar for goodez
4 months ago by
goodez460
United States
goodez460 wrote:
-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)
ADD COMMENTlink written 4 months ago by goodez460

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.

ADD REPLYlink written 3 months ago by znl20710

Or just filter the results after running pindel.

ADD REPLYlink written 3 months ago by goodez460
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