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Example analysis of human samples #57

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Oct 7, 2024
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Example analysis of human samples #57

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13 changes: 13 additions & 0 deletions docs/samples.md
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# Samples

A sample represents a set of changes to a reference genome. Take a simple vcf file with the following line:

```
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown G1 foo
m123 3 . CGA CA 1611.92 . . GT:DP:AD 1/1:56:0,53 . 1/1:56:0,53
```

This creates 3 new samples, `unknown`, `G1`, and `foo`. Each one of these samples will have its own copy of the
reference genome, and any changes specific to the sample. In this case, a sample can be thought of as mapping to
3 individuals (unknown, G1, and foo), but can be leveraged to model any set of changes. For example, a sample could
be a pooled sample with many changes, a clade, etc.
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