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bcgsc / straglr

Tandem repeat expansion detection or genotyping from long-read alignments
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Missing output #21

Closed topochico-one closed 1 year ago

topochico-one commented 1 year ago

Thank you for creating Straglr! Does Straglr produce output for repeats whose length is equal to the reference? I am asking this because the output for some repeats seems to be missing.

readmanchiu commented 1 year ago

Thanks for trying Straglr! If you run it in genotyping mode, it will size the loci given in the --loci bed file regardless of whether there is expansion. If you run it in genome scan mode, which you don't provide a bed file of target loci, then it will just report loci that have sizes larger than the reference genome by a threshold specified by --min_ins_size (default=100bp)

If you still see missing anticipated loci in either mode and cannot understand why, please report and I am happy to follow up on it.

topochico-one commented 1 year ago

Thanks for answering! I am running Straglr in genotyping mode. Some of my loci are probably missing because they have no coverage.