I am trying to apply some filters on whole exome sequencing data. Firstly I did the mapping using bwa and then I followed the proposed pipeline from GATK for Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode. As next step I am trying to apply the mappability filter <1 (based on 150bp reads) but I have confused with the term "mappability" . Can anyone tell me how can I calculate it ?
Thanks a lot, Maria