Pindel -M Option Is Confusing Me

Question

[Dalia]

Hi, I am running Pindel on with the -M option set to 30. According to Pindel documentation:

-M/--minimum_support_for_event Pindel only calls events which have this number or more supporting reads (default 3)

It was my understanding that a variant call would need at least 30 supporting reads for that call and would therefore also have a read depth of atleast 30. however, my resulting vcfs contain many calls that have a depth much lower than 30. For example this excerpt from a call on a multiple sample (3 samples) run:

GT:AD .:0 1/.:10 1/.:24

None of these have a depth >= 30... Does anyone have an explanation for this?

Thank you

Answer 1

[Devon Ryan]

Your example has 34 total reads covering that position. Much of the impetus for multisample calling is the ability to use information from multiple samples in making calls.

[Dalia]

thank you. This would also explain why I have so many more calls when I run Pindel with more samples!