Extract R1 Alignment Informations From Bam
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8.8 years ago

Hi,

Simple question : How to extract only aignment from R1 read from a bam file ?

Thanks

bam • 3.7k views
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8.8 years ago
samtools view -f 0x40 alignments.bam
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great that's perfect !

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This gives first in pair reads. But what about the reads which are not in pair i.e., R1 has aligned but not R2. I see R1's with flag 0 and 16 also.

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Then the aligner is setting the flags incorrectly. If a read came from a pair, then it should never have a flag of 0 or 16.

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