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alt ref maker. output length

Hi,

I'm trying to use the FastaAlternateReferenceMaker tool to make a new reference genome for read-mapping.

However, it merges all the chromosomes into one, simply called "1". Is there a command that allows chromosome/scaffold names to be maintained.

Also I guess that any frameshifts caused by insertions or deletions affect the base co-ordinates relative to the original assembly, making comparison with other data problematic.

Cheers,

Blue

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