Order of reads

[baozg]

Hi, @tobiasrausch

I just wondering what's logic for order of reads in the wally region? Could we specific the order ?

[tobiasrausch]

Wally uses the BAM index to parse through all reads of a given region. So the default order is coordinate-sorted and any other order would require storing the reads in memory. You can, of course, subset the BAM beforehand or split the BAM by a certain tag to visualize specific features of your data in separate panels.

[baozg]

Thanks for your explanation. In my case, I use contigs alignments from 66 samples. Is it possible to sort the order by read name? I don't think samtools sort -n could work in wally