one end of paired end reads disappeared in the aligned BAM file

[sotuamax]

Hi,

I use bwa to align paired-end reads to the reference genome. There are some cases, when the reads are labeled as paired alignment, and in the BAM file, only one end of the read can be found.

When transfer from BAM format to BEDPE format, there is always warning about the missing end for reads labeled as pair. I also use pysam to retrieve the reads, and in the case that the read and its mate information stored, its mate actually cannot be found in the BAM file.

Could you clarify what might cause this issue?

Many thanks.

Best,