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updated readme
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jonas-fuchs committed Nov 3, 2023
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Expand Up @@ -34,7 +34,8 @@ BAMdash automatically computes serveral statistics:
- for each track it computes recovery and mean coverage (set `-c` for the min coverage) for each element in the track
- if a `*.vcf` is provided it annotates `TRANSITION`/`TRANSVERSION` and type of exchange (`SNP`, `DEL`, `INS`)

If a `*.gb`and `*.vcf` is provided BAMdash computes the aminoacid exchange and the effect in the CDS (inspired by but not as powerful as [snpeff](http://pcingola.github.io/SnpEff/snpeff)). SNP and INDEL vcf annotation supports:
If a `*.gb`and `*.vcf` is provided BAMdash computes if the mutations could have been caused by APOBEC deamination.
Moreover, it annotates the aminoacid exchange and the effect in the CDS (inspired by but not as powerful as [snpeff](http://pcingola.github.io/SnpEff/snpeff)). SNP and INDEL vcf annotation supports:

- `START_LOST`: INDEL or SNP start at the CDS and result in a start loss
- `STOP_LOST`: INDEL or SNP result in the loss of the stop codon
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