Get rid of multimapped and unmapped reads for snp calling improvement

Question

[Denis]

I'm doing snp calling for several projects in which either BWA or Bowtie2 was used to map reads to the reference genome. I use only reads with mapping quality >= 20 in my workflow. Can i be completely sure by doing so that all the multimapped and unmapped reads are not used for snp calling or i have to use other approach to filter out these reads? I.e. may multimapped and unmapped reads have the mapping quality >=20 in the BAM file produced by BWA or Bowtie2 aligners?

[ATpoint]

Multimappers have usually a MAPQ of zero and unmapped reads have no MAPQ at all.