Mappability calculation based on 150 bp reads after mapping with bwa
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6 months ago

Hi,

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

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