Question: Are bwa alt contigs controlled purely by idxbase.alt?
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gravatar for d-cameron
21 days ago by
d-cameron2.2k
Australia
d-cameron2.2k wrote:

What is the source of bwa ALT alignment? The documentation indicates that:

bwa reads the ALT contig names from "idxbase.alt"

Does this means that the index itself contains no information about ALT contigs? Would I be able to JIT assign a different set of ALT contigs for different samples without having to rebuild to the index?

bwa • 78 views
ADD COMMENTlink written 21 days ago by d-cameron2.2k
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