.csi indexes

[lorenzopanca5]

Hi everyone,

I am trying to use HapScanner to compare an "assembly vs assemly" alignment (ref is durum wheat and query is barley) obtained with NUCmer, in order to assess the alleles at some position/sites that I have (VCF format).
The only thing is that due to the length of some chromosome I can not make .bai indexes of the alignments.
Does HapScanner works anyway with .csi indexes?

Thanks for your answer,

Lorenzo