The output format of pindel

[zhangnan0107]

Hi,
I got a question referring to "sample name + 6 numbers" pattern and the number for AD tag when looking through the output files from pindel. Could you please help me out?

First, the 6 numbers following sample name, I have already read the explanations from b706fba. Still confused about the first 2 numbers, are they the depth (ref + alt) or only the ref count?

By the way, just want to clear up that the larger one of these 2 numbers will be used as the first number in AD tag when converting pindel result to vcf file, right?

Screenshot below is the text I read, as you can see, both "read depth" and "reference coverage" are used in describing the first 2 numbers, so which one is correct, the ref OR ref + alt

Thanks,
Nan