Issues

• Sniffles 2.8.1 bug with handling vcf.gz files

  fritzsedlazeck/Sniffles#613 · Filter by author VasLem opened on Sep 16, 2026
  2

• Possible regression: same-strand translocations give no BND call at all in v2.8.0

  bugenhancement
  fritzsedlazeck/Sniffles#612 · Filter by author awgymer opened on Aug 31, 2026 · 2.9
  

• Brand New User Question. Having trouble using Sniffles2 to find inversion differences between two individuals. Help?

  fritzsedlazeck/Sniffles#605 · Filter by author NateHanby opened on Apr 11, 2026

• Sniffles2 calls unrealistically large deletions (>60 Mb) with PASS filter in clinical WGS

  fritzsedlazeck/Sniffles#603 · Filter by author enes-ak opened on Mar 30, 2026

• Massive unrealistic DUP in Sniffles 2.7 output

  fritzsedlazeck/Sniffles#600 · Filter by author Dario-Galanti opened on Dec 19, 2025

• clarification of coverage in Sniffles2 VCF

  fritzsedlazeck/Sniffles#598 · Filter by author svedwards opened on Nov 16, 2025
  4

• Support for MATEID when reporting breakends with known mates?

  enhancement
  fritzsedlazeck/Sniffles#589 · Filter by author roland-ewald opened on Sep 29, 2025 · 2.9
  1

  

• Parameter suggestions for Sniffles to detect transposable elements from ONT data

  fritzsedlazeck/Sniffles#578 · Filter by author amarkez opened on Aug 13, 2025
  1

• Wrong insertion can be inferred from split alignments

  fritzsedlazeck/Sniffles#561 · Filter by author HillJamie opened on May 14, 2025

• Expectations regarding discrepancies in individual vs population called VCFs

  fritzsedlazeck/Sniffles#546 · Filter by author stallmanGEL opened on Mar 4, 2025
  4

  

• Difference between SUPPORT, DV and RNAMES

  bugenhancement
  fritzsedlazeck/Sniffles#496 · Filter by author kamilafras opened on Jul 17, 2024 · 2.9
  4

  

• Detection of Reciprocal BNDs

  enhancement
  fritzsedlazeck/Sniffles#486 · Filter by author Carly-KT opened on Jun 11, 2024 · 2.9
  

• Enhancement: sample ID handling

  enhancement
  fritzsedlazeck/Sniffles#443 · Filter by author ptrebert opened on Dec 1, 2023
  2

• Compatibility issue for consensus creation

  fritzsedlazeck/Sniffles#442 · Filter by author Mossy-Frog opened on Nov 27, 2023
  12

• Incomplete RNAMES?

  bug
  fritzsedlazeck/Sniffles#437 · Filter by author weishwu opened on Oct 26, 2023

• Population /Trio merging snf file - SUPP_VEC=only zeroes

  fritzsedlazeck/Sniffles#436 · Filter by author sofiabanu opened on Oct 23, 2023
  1

  

• Fully supported CRISPR edit not detected.

  fritzsedlazeck/Sniffles#429 · Filter by author caonetto opened on Sep 25, 2023
  6

• Why are BNDs filtered differently in primary and supplementary alignments?

  fritzsedlazeck/Sniffles#426 · Filter by author HillJamie opened on Sep 6, 2023
  

• output vcf DR correspond to the number of alignments not the read numbers

  fritzsedlazeck/Sniffles#418 · Filter by author ErminZ opened on Aug 11, 2023

• BND alt alleles are incorrect - and an attached fix

  fritzsedlazeck/Sniffles#413 · Filter by author HillJamie opened on Jul 7, 2023

• Multisample Calling with BND (translocation) variants

  fritzsedlazeck/Sniffles#412 · Filter by author tbenavi1 opened on Jul 5, 2023
  1

• Hard clipping is not fully supported

  fritzsedlazeck/Sniffles#409 · Filter by author HillJamie opened on Jun 22, 2023

• Typo in calculating mean_svlen for merging of clusters

  enhancement
  fritzsedlazeck/Sniffles#407 · Filter by author HillJamie opened on Jun 16, 2023

• Possible bug: first cluster can only be merged once

  fritzsedlazeck/Sniffles#406 · Filter by author HillJamie opened on Jun 16, 2023
  1

  

• VCF output insertions alternative alleles incorrect

  fritzsedlazeck/Sniffles#402 · Filter by author dennishendriksen opened on Jun 2, 2023
  1