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Advice on VAF filtering thresholds for Inbred Lines using ONT R9.4.1 data

Status: Open.

#217 In kishwarshafin/pepper;

· anastasiatete444-lgtm opened on Dec 22, 2025

Expected variants not called in intermediate VCF, causing ‘No valid VCF entries found!’ error in Margin step

Status: Open.

#215 In kishwarshafin/pepper;

· Keidai-Miyakawa-HU opened on Nov 27, 2025

Update DeepVariant to v1.9.0

Status: Open.

#214 In kishwarshafin/pepper;

· tetedange13 opened on Oct 8, 2025

T2T reference

Status: Open.

#213 In kishwarshafin/pepper;

· Lucie02Rose opened on Apr 3, 2025

TRUTH_VCF

Status: Open.

#212 In kishwarshafin/pepper;

· thangnx1012 opened on Feb 27, 2025

No variants found during rerun

Status: Open.

#211 In kishwarshafin/pepper;

· dmjask opened on Jan 23, 2025

Runtime on CCS reads

Status: Open.

#210 In kishwarshafin/pepper;

· Lionward opened on Nov 5, 2024

required "-m/--model_path"

Status: Open.

#209 In kishwarshafin/pepper;

· KANGYUlab opened on Oct 30, 2024

PEPPER-Margin-DeepVariant takes more cores than limit

Status: Open.

#208 In kishwarshafin/pepper;

· martabaragli opened on Jun 17, 2024

Error in margin phase :No valid VCF entries found!

Status: Open.

#207 In kishwarshafin/pepper;

· kch4221 opened on May 24, 2024

Issue with docker GPU

Status: Open.

#205 In kishwarshafin/pepper;

· martabaragli opened on Apr 4, 2024

phasing between R9 and R10 data

Status: Open.

#204 In kishwarshafin/pepper;

· Yijun-Tian opened on Feb 28, 2024