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DeepVariant variant caller

enhancementNew feature or requestNew feature or request

Status: Open.

#295 In nf-cmgg/smallvariants;

· ToonRosseel opened on Dec 8, 2025

MSI check not completely ok

bugSomething isn't workingSomething isn't working

Status: Open.

#290 In nf-cmgg/smallvariants;

· mvheetve opened on Oct 28, 2025

gdb optimization

enhancementNew feature or requestNew feature or request

Status: Open.

#274 In nf-cmgg/smallvariants;

· matthdsm opened on May 27, 2025

evaluate <code>GLnexus</code> for joint variant calling

enhancementNew feature or requestNew feature or request

Status: Open.

#263 In nf-cmgg/smallvariants;

· matthdsm opened on Mar 27, 2025

explore <code>reblockgvcf</code> to further compress gvcf output

enhancementNew feature or requestNew feature or request

low-priorityLow priority issues (Don't focus on these for the next release)Low priority issues (Don't focus on these for the next release)

Status: Open.

#260 In nf-cmgg/smallvariants;

· matthdsm opened on Jan 28, 2025

Benchmark vep annotation with/without ensembl-xs

enhancementNew feature or requestNew feature or request

Status: Open.

#254 In nf-cmgg/smallvariants;

· tomiles opened on Jan 22, 2025

VEP: use bgzipped fasta reference

enhancementNew feature or requestNew feature or request

Status: Open.

#244 In nf-cmgg/smallvariants;

· matthdsm opened on Dec 6, 2024

Add somalier ancestry

enhancementNew feature or requestNew feature or request

low-priorityLow priority issues (Don't focus on these for the next release)Low priority issues (Don't focus on these for the next release)

Status: Open.

#241 In nf-cmgg/smallvariants;

· nvnieuwk opened on Nov 26, 2024

GATK is slow, investigate alternatives to speed things up

enhancementNew feature or requestNew feature or request

low-priorityLow priority issues (Don't focus on these for the next release)Low priority issues (Don't focus on these for the next release)

Status: Open.

#211 In nf-cmgg/smallvariants;

· matthdsm opened on Oct 17, 2024

Explore <code>VariantRecalibrator</code> and <code>ApplyVQSR</code> for better filtering

enhancementNew feature or requestNew feature or request

low-priorityLow priority issues (Don't focus on these for the next release)Low priority issues (Don't focus on these for the next release)

Status: Open.

#166 In nf-cmgg/smallvariants;

· nvnieuwk opened on Mar 13, 2024

Add somatic calling

enhancementNew feature or requestNew feature or request

low-priorityLow priority issues (Don't focus on these for the next release)Low priority issues (Don't focus on these for the next release)

Status: Open.

#141 In nf-cmgg/smallvariants;

· nvnieuwk opened on Jul 12, 2023

Investigate non-coding variants annotation

enhancementNew feature or requestNew feature or request

low-priorityLow priority issues (Don't focus on these for the next release)Low priority issues (Don't focus on these for the next release)

Status: Open.

#127 In nf-cmgg/smallvariants;

· nvnieuwk opened on Jun 8, 2023