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I am not aware of a benchmark study that would allow me to pinpoint the best resource, but a very good one that I use frequently is <https:…
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You'll have to re-sequence that locus. Or look at replicate samples that are expected to have the same variants.
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The HBC Training link gives most details you'll need.
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Seconding this, you can also read a bit more about this [here](https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Referen…
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How many contigs do you have in your fasta file?
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I have managed to solve my problems with the details in this link:
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what exactly do you want to show about them. do you want to show the order in which they arose? or epistasis between them> ? or any other p…
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