Get rid of multimapped and unmapped reads for snp calling improvement
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7 months ago
Denis ▴ 230

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?

genome mapping SNP Illumina • 290 views
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Multimappers have usually a MAPQ of zero and unmapped reads have no MAPQ at all.