Issues

• Reference GFF frame/phase hardcoded to 1 instead of 0 for CDS features, shifting all protein-level annotations

  tseemann/snippy#631 · Filter by author snnisa opened on Sep 19, 2026

• SNPs between strains instead of compared to reference

  tseemann/snippy#630 · Filter by author aperreault opened on Jul 21, 2026

• UseGalaxy fatal error 2 ()

  tseemann/snippy#629 · Filter by author L-R-935 opened on May 16, 2026

• Snippy / Samtools issue in conda. Remove version cehcks?

  tseemann/snippy#628 · Filter by author KasperThystrup opened on Jan 9, 2026

• Snippy discards variants present in heterozygosity even if they are majority

  tseemann/snippy#627 · Filter by author victor5lm opened on Dec 26, 2025
  2

• Issue with shredding contigs

  tseemann/snippy#619 · Filter by author djwbdjg opened on Oct 10, 2025

• Questions regarding the software output results

  tseemann/snippy#617 · Filter by author lanlan0210 opened on Jun 17, 2025

• Failure to extract bases from fasta reference

  tseemann/snippy#616 · Filter by author cizydorczyk opened on Jun 10, 2025

• Unfixed_SNPs_Calling

  tseemann/snippy#615 · Filter by author Tuberculosis-Public-Health-Lab opened on Jun 10, 2025

• Region limitation error in Snippy final.vcf

  tseemann/snippy#614 · Filter by author KuBaLa-biomedicine opened on May 19, 2025

• Error trying to use snippy with GBK reference: snps.log

  tseemann/snippy#613 · Filter by author raeldesu opened on Apr 25, 2025

• Error following samclip and bam_sort_core

  tseemann/snippy#611 · Filter by author mweberr opened on Mar 17, 2025

• PackagesNotFoundError unable to install snp-sites and snippy via bioconda

  tseemann/snippy#610 · Filter by author gloriajzhou opened on Mar 13, 2025
  2

• Error in snippy-vcf_to_tab when features overlap

  tseemann/snippy#609 · Filter by author pablo-aja-macaya opened on Feb 24, 2025
  3

• Zero variants identified using snippy 4.6.0, 4.6.0-5 recipe on bioconda - error due to "vt normalize" at the filtering step

  tseemann/snippy#608 · Filter by author stefcamp opened on Feb 4, 2025
  1

• Homebrew install fails due to dependency: openssl@1.1 has been disabled because it is not supported upstream! It was disabled on 2024-10-24.

  tseemann/snippy#607 · Filter by author joelewis101 opened on Jan 28, 2025

• Error message: Got a sequence without letters. Could not guess alphabet

  tseemann/snippy#606 · Filter by author Alessandra-23 opened on Jan 22, 2025

• snippy-multi "No SNPs were detected

  tseemann/snippy#605 · Filter by author beryl-au opened on Jan 9, 2025
  2

• No variants found when expected - No warnings

  tseemann/snippy#604 · Filter by author suhanyaPrasad opened on Dec 15, 2024

• freebayes option "--region" in present in vcf file but not in log file freebayes command

  tseemann/snippy#603 · Filter by author sachiwije opened on Nov 26, 2024

• Snippy tool successfully run but no variants identified which expected to be found

  tseemann/snippy#602 · Filter by author imran-24-du opened on Nov 19, 2024
  1

• Error Installing with linuxbrew

  tseemann/snippy#600 · Filter by author joaomatos02 opened on Nov 5, 2024
  1

• Raw VCF

  tseemann/snippy#599 · Filter by author sydelstan opened on Nov 4, 2024

• samtools markdup: error, no ms score tag

  tseemann/snippy#598 · Filter by author lusacristan opened on Sep 18, 2024
  5

• No variants found

  tseemann/snippy#597 · Filter by author BlackMonolith opened on Aug 27, 2024
  2