Hi,
I am using VIRUSBreakend for detecting viral integration in human WGS(30X) samples.

I used the default parameters in the virusbreakend.sh script.

I got the output file in .vcf format and converted to excel for examples.(provided in the preview).

I have the following question regarding the output file:

1: What is the critera of FILTER? I found that the values are enough high in the QUAL(684.91, 357.52, 276.53), but they regarded as LOW-QUAL in the FILTER column. And, is it possible to change the filtering criteria and make it more strict?

2: I need to the supporting viral read count and human read count at breakpoint. I wonder RP,SR,REF,RF,VF FORAMT(or INFO) vaues are corresponding (representing) to these breakpoint values?