I am working on freeBayes pipeline for variant calling on BRCA sequence aligned with BWA and I have some questions: 1. The pipeline of FreeBayes bayesian genetic variant detector (Galaxy Version 18.104.22.168-3) includes variant recalibration?? 2. I am not sure about the cutoff of the variant quality filters. I am using the following suggested hard filters (Presentation from Erik Garrison) a. QUAL > 1 b. QUAL / AO > 10 c. SAF > 0 & SAR > 0 d. RPR > 1 & RPL > 1 Someone has a better suggestion about the filters?? I am doing the filters over the vcf file resulted as output, but I am not sure how to set them in the freebayes prompt of galaxy.
I would appreciate any suggestios, Thanks Sandra Romero