MAPQ filtering

[Antonis Koussounadis]

Dear Tobias,

Thanks for developing, maintaining Delly and answering user's questions in this user group.
I am using Delly to call SVs in standalone WGS germline samples. Therefore I cannot take advantage of the filtering step, since I need 20 samples or so in a merged VCF.
Still, I have to filter the high number of calls and I use the following strategy:
Keep calls that satisfy the following criteria
     1. genotype is not 0/0
     2. INFO/PE + INFO/SR >5
     3. FORMAT/GQ>20
     4. QUAL>100
and I am wondering if an additional filter:
     5. MAPQ>0 , would make sense.
I would be grateful to have your opinion on this filtering strategy and any suggestions you may have.

Kind regards

Antonis