paired-end view

[Tgrandis]

I use alfred to extract reads aligned to a particular region from a bam file. My bam file is derived from Illumina paired-end read data. Currently I can extract all reads mapping to a particular location, which is more of less what one would see in IGV individual read view. However, IGV has the option to view reads as paired and I would really like to be able to extract the reads from a bam file as such. Would it be possible to provide that option in alfred? It would greatly help me and maybe some others as well. Thanks in advance.

[tobiasrausch]

For the consensus subcommand this would not work because reads need to overlap the input position. alfred computes a classical multiple sequence alignment around that input position.