Export alignment groups?

[Lizzy Wilbanks]

Hi folks,

Apologies if this is documented somewhere and I missed it...

I've used "Group alignments by base" to create hapotype groups for my aligned pacbio HiFi reads.  What I'd love to be able to do now is to export the names of reads in each group from a region of interest.  I've used "Export Alignments" and gotten a "VisibleData.sam" file, but so far as I can tell, this is all the reads in that field of view, without the group information included.  

Any tips much appreciated!

Thanks,

Lizzy

[igv-help]

Hi Lizzy,

Sorry - you can't do that in IGV.

Helga