Question about samtools view flags (paired reads vs. properly paired reads)
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23 days ago
mrk • 0

What exactly does it mean for a read to be 'mapped in a proper pair' (flag 0x2) as opposed just paired reads (0x1)? I have a bam file where, when I use -f 0x2, I get no output. Does this mean the reads weren't aligned or something?

samtools • 241 views
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23 days ago

paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the sequencer.

mapped in a proper pair= the two sam records of a pair are mapped on the sam chromosome, at a good distance, mapped on forward and reverse strand (like a PCR, but it's not a PCR)

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Thanks. What determines what constitutes a good distance? I have some targeted panel data and looking at flagstat, almost all reads are paired, mapped, and 'with itself and mate mapped' but 0 are properly paired. The distance might be the issue?

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Thanks. What determines what constitutes a good distance?

I think tools like BWA use the median distance for each chunk of processed data

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