From 8f569c21fc964e642348c9ab0d9961b6c0d49a66 Mon Sep 17 00:00:00 2001 From: zhenxian Date: Wed, 20 Dec 2023 17:02:29 +0800 Subject: [PATCH] Update README.md --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 4501b3c..780848f 100644 --- a/README.md +++ b/README.md @@ -21,6 +21,8 @@ Clair3 is the 3rd generation of [Clair](https://github.com/HKU-BAL/Cl 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). +For somatic variant calling using paired tumor/normal samples, please try [ClairS](https://github.com/HKU-BAL/ClairS). + ---- ## Contents @@ -59,6 +61,8 @@ Clair3 is published at [Nature Computational Science](https://rdcu.be/c1TPa), an ---- ## Latest Updates +*v1.0.5 (Dec 20, 2023)* : 1. Fixed the issue showing wrong multi-allelic AF when read coverage is excessively high ([#241](https://github.com/HKU-BAL/Clair3/issues/241)). 2. Added `--base_err` and `--gq_bin_size` options that can resolve the problem of having excessive GT ./. in GVCF output ([#220](https://github.com/HKU-BAL/Clair3/issues/220)). 3. Modified logs ([#231](https://github.com/HKU-BAL/Clair3/issues/231), [#225](https://github.com/HKU-BAL/Clair3/issues/225)) + *v1.0.4 (Jul 11, 2023)* : 1. Added showing command line and reference source in output VCF header. 2. Fixed a bug in showing the AF tag for 1/2 genotypes. 3. Added AD tag output. *v1.0.3 (Jun 20, 2023)* : 1. Colon ':' is now allowed in reference sequence name ([#203](https://github.com/HKU-BAL/Clair3/issues/203)). @@ -428,6 +432,8 @@ Instructions are given as an answer to issue [#149](https://github.com/HKU-BAL/C --call_snp_only EXPERIMENTAL: Call candidates pass SNP minimum AF only, ignore Indel candidates, default: disable. --enable_long_indel EXPERIMENTAL: Call long Indel variants(>50 bp), default: disable. --keep_iupac_bases EXPERIMENTAL: Keep IUPAC reference and alternate bases, default: convert all IUPAC bases to N. + --base_err=FLOAT EXPERIMENTAL: Estimated base error rate when enabling gvcf option, default: 0.001. + --gq_bin_size=INT EXPERIMENTAL: Default gq bin size for merge non-variant block when enabling gvcf option, default: 5. ``` #### Call variants in a chromosome