How we can use genmap scores ?

[AstrMary]

Hallo,

thank you for your tool! I used it according your manual so I have a txt file with mappability score for my reference genome (150,2) Could I use the produced scores to filter my variants?

My data are whole exome sequencing I used bwa aligner and then I followed the instructions of GATK tool in order to produce a vcf file

I am little bit confused how I can use the mappability score to filter my variants

Any help would welcome! Thanks a lot, Maria