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Missing SNPs from high depth file

Status: Open.

#397 In HKU-BAL/Clair3;

· danielwood1992 opened on Jul 17, 2025

How to speed up clair3?

Status: Open.

#393 In HKU-BAL/Clair3;

· ChillarAnand opened on Jul 4, 2025

Favor Pileup over Full_alignment when SNP has high QUAL and Full alignment incorrectly assigns as Refcall

enhancementNew feature or requestNew feature or request

Status: Open.

#360 In HKU-BAL/Clair3;

· wshropshire opened on Feb 13, 2025

[ERROR] No full-alignment output for file (Illumina)

enhancementNew feature or requestNew feature or request

Status: Open.

#350 In HKU-BAL/Clair3;

· dgslos opened on Dec 17, 2024

show more allele counts in INFO

enhancementNew feature or requestNew feature or request

Status: Open.

#320 In HKU-BAL/Clair3;

· hoyonh opened on Jul 12, 2024

choose pileup call over full-alignment call if pileup call has 1) a way higher QUAL, 2) is an indel

enhancementNew feature or requestNew feature or request

Status: Open.

#318 In HKU-BAL/Clair3;

· drtconway opened on Jul 2, 2024

Incorrect SNP representation when it overlaps a deletion

enhancementNew feature or requestNew feature or request

Status: Open.

#272 In HKU-BAL/Clair3;

· ymcki opened on Feb 23, 2024

Send adjacent SNP and Indel candidates both to full-alignment model

enhancementNew feature or requestNew feature or request

Status: Open.

#260 In HKU-BAL/Clair3;

· haraldgrove opened on Jan 10, 2024