Get rid of multimapped and unmapped reads for snp calling improvement
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?
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