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aquaskyline authored Dec 20, 2022
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Expand Up @@ -19,7 +19,7 @@ Clair3 is a germline small variant caller for long-reads. Clair3 makes the best

Clair3 is the 3<sup>rd</sup> generation of [Clair](https://github.com/HKU-BAL/Clair) (the 2<sup>nd</sup>) and [Clairvoyante](https://github.com/aquaskyline/Clairvoyante) (the 1<sup>st</sup>).

A short preprint describing Clair3's algorithms and results is at [bioRxiv](https://www.biorxiv.org/content/10.1101/2021.12.29.474431v1).
Clair3 is published at [Nature Computational Science](https://rdcu.be/c1TPa), and available as a preprint at [bioRxiv](https://www.biorxiv.org/content/10.1101/2021.12.29.474431v2).

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Clair3 supports both VCF and GVCF output formats. Clair3 uses VCF version 4.2 specifications. Specifically, Clair3 adds a `P` INFO tag to the results called using a pileup model, and a `F` INFO tag to the results called using a full-alignment model.
Clair3 outputs a GATK-compatible GVCF format that passes GATK's `ValidateVariants` module. Different from DeepVariant that uses `<*>` to represent any possible alternative allele, Clair3 uses `<NON_REF>`, the same as GATK.
Clair3 outputs a GATK-compatible GVCF format that passes GATK's `ValidateVariants` module. Different from DeepVariant that uses `<*>` to represent any possible alternative allele, Clair3 uses `<NON_REF>`, the same as GATK.

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