Delly Stringent filters in call-gSV pipeline

[Faizal-Eeman]

@tyamaguchi-ucla

I see we don't currently have Delly stringent filters applied to the pipeline like we have in call-sSV.

We currently have mapping quality as a filter for Delly in call-gSV pipeline. See the template.config below,

pipeline-call-gSV/pipeline/config/template.config

Line 34 in 0ba5d1e

map_qual = 20 // min. paired-end (PE) mapping quality for Delly

Did we exclude the other two stringent filters, mad_cutoff and min_clique_size for a specific reason? Or Can I go ahead and add these filters in this pipeline? These filters essentially improve the runtime.