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replace literal HTML entity
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tseemann committed Nov 9, 2019
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -300,7 +300,7 @@ Character | Meaning
`-` | Zero coverage in this sample **or** a deletion relative to the reference
`N` | Low coverage in this sample (based on `--mincov`)
`X` | Masked region of reference (from `--mask`)
`n` | Heterozygous or poor quality genotype (has `GT=0/1` or `QUAL<--minqual` in `snps.raw.vcf`)
`n` | Heterozygous or poor quality genotype (has `GT=0/1` or `QUAL < --minqual` in `snps.raw.vcf`)

You can remove all the "weird" characters and replace them with `N` using the included
`snippy-clean_full_aln`. This is useful when you need to pass it to a tree-building
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