I have a pair end bam. And I want to know whether the record is the first in pair or the second in pair. I use the julia package called XAM.jl. using XAM bamfile="..." reader=open(BAM.Reader,bamfile) mapped_chr1 = Iterators.filter(x->(BAM.refname(x)=="chr1"), reader) for record in mapped_chr1 p…

You’re on the right track, and Explain SAM Flags is a great resource. You can query the flag properties using boolean algebra. When a property is set, the flag value anded with the property value will equal the property value. Using a flag of 163 as an example. julia> flag = UInt8(163) # BAM.fla…

How do I distinguish the first in pair and second in pair in pair end bam using XAM?

Specific Domains Biology, Health, and Medicine

CiaranOMara January 8, 2023, 5:15am 3

I thought the following video neatly linked the flag back to the SAM Format Specification.

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How do I distinguish the first in pair and second in pair in pair end bam using XAM?

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