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parseVEP issue with VCF & GENCODE CSQ

Status: Open.

#943 In uclahs-cds/package-moPepGen;

· zhuchcn opened on Oct 11, 2025

callVariant generates fusion derived peptides > 25mers when using --cleavage-rule None

Status: Open.

#929 In uclahs-cds/package-moPepGen;

· Geneece opened on Jul 10, 2025

Variant Phasing

Status: Open.

#924 In uclahs-cds/package-moPepGen;

· zhuchcn opened on Jul 1, 2025

[parseVEP] Support complex indel as MNV

Status: Open.

#909 In uclahs-cds/package-moPepGen;

· zhuchcn opened on Apr 5, 2025

Documentation suggestion for external users

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#895 In uclahs-cds/package-moPepGen;

· lydiayliu opened on Feb 19, 2025

STAR junction file support

Status: Open.

#888 In uclahs-cds/package-moPepGen;

· hsiaoyi0504 opened on Feb 11, 2025

parseREDItools Does Not Write Gene Symbol into GVF

Status: Open.

#884 In uclahs-cds/package-moPepGen;

· zhuchcn opened on Dec 4, 2024

Cache genome sequence

Status: Open.

#860 In uclahs-cds/package-moPepGen;

· zhuchcn opened on Mar 18, 2024

Additional testing of merged MNVs

Status: Open.

#822 In uclahs-cds/package-moPepGen;

· lydiayliu opened on Nov 8, 2023

Alternative Way to Handle Trypsin Exception

enhancementNew feature or requestNew feature or request

Status: Open.

#821 In uclahs-cds/package-moPepGen;

· zhuchcn opened on Oct 26, 2023

Unconsistency between splitFasta and summarizeFasta

enhancementNew feature or requestNew feature or request

Status: Open.

#819 In uclahs-cds/package-moPepGen;

· zhuchcn opened on Oct 24, 2023

Support use of junction files from RNA-seq alignment tools

enhancementNew feature or requestNew feature or request

Status: Open.

#757 In uclahs-cds/package-moPepGen;

· lydiayliu opened on Jun 29, 2023