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tobiasrausch / alfred

BAM Statistics, Feature Counting and Annotation
https://www.gear-genomics.com/alfred/
BSD 3-Clause "New" or "Revised" License
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paired-end view #94

Open Tgrandis opened 1 year ago

Tgrandis commented 1 year ago

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 commented 1 year ago

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.