Question: Pindel -x option
0
gravatar for znl207
9 weeks 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 9 weeks ago by goodez420 • written 9 weeks ago by znl20710
0
gravatar for goodez
9 weeks ago by
goodez420
United States
goodez420 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 9 weeks ago by goodez420

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 5 weeks ago by znl20710

Or just filter the results after running pindel.

ADD REPLYlink written 5 weeks ago by goodez420
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1176 users visited in the last hour