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Old 06-19-2015, 11:29 AM   #1
Location: US

Join Date: Jan 2013
Posts: 77
Default BWA properly paired reads are not really properly paired?

I selected properly paired (and mapq>=4) reads from BWA alignment by running:
samtools view -h -f 2 -q 4 -b
Flagstat shows that this did remove most of the reads that have mates on different chr. However, several remain:
5 + 0 with mate mapped to a different chr
4 + 0 with mate mapped to a different chr (mapQ>=5)
Why is this?
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