BWA .alt index file

Question

[tejaswikoganti]

Hello, I am working with canine reference and trying to use BWA for alignment. I understand that we have to generate index files for reference before running BWA-mem so I used bwa index to generate index files. I got 5 files as a result and those did not include .alt file. After reading the documentation on alt-aware mode, I would like to use the .alt file in BWA to correctly map all the multiply mapping reads. If there is documentation out there on how to generate .alt file that I missed, I would really appreciate if someone could point me to it.

[glmeeks]

Hi, did you figure out how to generate an .alt index file?

Answer 1

[brunobsouzaa]

Maybe this can help How to create .alt index file?