BWA .alt index file · Biostar

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BWA .alt index file

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.

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updated 3.1 years ago by Ram

• written 6.3 years ago by tejaswikoganti

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

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written 4.3 years ago by glmeeks •

1 answer

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

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written 6.3 years ago by brunobsouzaa

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