why bwa-mem only return one read with pair-read end

Question

[QX]

Hi all,

I have a very basic question. We introduce read1 and read2 into the bwa-mem; why does in the bam file output, they only give 1 sequence in return?

[GenoMax]

Have you tried name sorting the alignment file and/or viewing the alignment in IGV? Paired-end reads are not guaranteed to be next to each other in the file. There may be a discordant alignment for the read pair (because the read captures a chromosomal breakpoint). Or the second read has not mapped.