Extract improperly paired read from BAM file
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2.0 years ago
godth13teen ▴ 70

Hi, I want to do manual checking on my BAM file after getting the statistic from samtools flagstat. I tried to extract the improperly paired read but failed to do so far.

I tried to use awk to extract read not contain 2 flagstat, but it's not working because the flagstat is bitwise and combined.

Thank you for your advice.

alignment • 603 views
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2.0 years ago

Don't use awk. Use samtools view.

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