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Does the FastaAlternateReferenceMaker also work for simple sequence repeats?

I_MI_M Member

I have questions regarding the FastaAlternateReferenceMaker. Does it also work for Simple Sequence Repeats? How long can the repetitions be, to still be intergrated in the new reference?

Many thanks in advance!


  • bshifawbshifaw Member, Broadie, Moderator admin

    Hi @I_M ,
    All the caveats of FastaAlternateReferenceMaker are listed in the tool docs

    • If there are multiple variants that start at a site, it chooses one of them randomly.
    • When there are overlapping indels (but with different start positions) only the first will be chosen.
    • This tool works only for SNPs and for simple indels (but not for things like complex substitutions).

    I haven't had a chance to observe the tools results on repeats but this wouldn't seem problematic since the tool simply "replaces the reference bases at variation sites with the bases supplied in the corresponding callset records". Let us know what you observe.

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