tseemann/snippy

Issues

• samtools markdup: error, no ms score tag

  #598 opened 2 months ago by lusacristan
  4

• No variants found

  #597 opened 3 months ago by BlackMonolith
  1

• snippy-multi ERROR: Can't open --ref BZ100/ref.fa

  #591 opened 5 months ago by makerer5
  8

• no. variants normalized

  #554 opened a year ago by cpplyqz
  3

• Low variant counts due to poor mapping or low coverage (?)

  #596 opened 3 months ago by priscalim00
  1

• Snippy: no output - identification of 0 variants and empty csv file

  #580 opened 10 months ago by ZoseJapata
  4

• Snippy not identifying rRNA SNPs (presumably due to conserved region?)

  #595 opened 3 months ago by BGemler
  0

• homebrew snippy installation finding incorrect perl binaries

  #594 opened 4 months ago by paulsenlab
  0

• Need bcftools --version >= 1.7 but you have 0 - please upgrade it

  #592 opened 4 months ago by NoamanJane
  1

• Snippy fails with genbank file

  #581 opened 10 months ago by mesti90
  4

• Got broken pipeline when running freebayes-parallel

  #561 opened a year ago by buihoangphuc412
  28

• why snippy generated variations less than snp-sites generated from core gene alignment?

  #590 opened 6 months ago by Zjianglin
  0

• samtools excluded most reads

  #574 opened a year ago by DorothyTamYiLing
  1

• freebayes-parallel Error

  #585 opened 9 months ago by xxxxxxsf
  1

• bcftool error

  #586 opened 8 months ago by SaraRHenderson
  1

• Request to troubleshoot bcftools error encountered while installing snippy in macOS Sonoma 14.4.1

  #589 opened 6 months ago by Jeewan-Thapa
  1

• Snippy can't read my assembly.fasta files

  #588 opened 7 months ago by dianaespadinha
  0

• Unable to calculate estimated library size: samtools markdup

  #587 opened 7 months ago by Shyamili09
  0

• vcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory vcfuniq: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory

  #584 opened 9 months ago by shangguan77
  3

• snippy-multi ERROR: Could not find .aligned.fa/.vcf in 100AEA1

  #572 opened a year ago by drhoads
  5

• Cannot install snippy due to bcftools?

  #583 opened 9 months ago by Xiongqi1114
  0

• ™ BrokenPipeError: [Errno 32] Broken pipe, can you please assist for this error

  #582 opened 10 months ago by EtienneNtumba
  1

• libtabixpp.so.0: cannot open shared object file

  #570 opened a year ago by DorothyTamYiLing
  4

• How to use snippy with pre-indexed reference

  #579 opened 10 months ago by minhdz09
  0

• Which alignment file can be used to create SNP matrix for clonal studies

  #578 opened a year ago by Firdoos071
  0

• Error running snippy

  #577 opened a year ago by AlbaMunozSanta
  0

• Files to test an installation

  #576 opened a year ago by jolespin
  0

• Number of contigs mismatch when generated from gbk file

  #575 opened a year ago by sreerampeela
  0

• Possible to set %identity of reads mapping to ref?

  #573 opened a year ago by appliedmicrobiologyresearch
  0

• Using Snippy to identify the delete which is about 1kb to 5kb

  #571 opened a year ago by TaoCheng98
  0

• error

  #566 opened a year ago by sekhwal
  4

• Can't run snippy-core with more than 1 CPU

  #569 opened a year ago by Alejandro-PI
  0

• snippy core took isolate as ref

  #563 opened a year ago by tbazilegith
  1

• Missing build items in conda OR freebayes-parrallel problem

  #565 opened a year ago by hughgifford
  2

• bug: contig mode does not find all snps

  #564 opened a year ago by Saarkie
  0

• .gb file not working as the reference and with fasta reference, FTYPE,STRAND,NT_POS, AA_POS , EFFECT,LOCUS_TAG,GENE PRODUCT are empty columns

  #546 opened 2 years ago by absartalat
  4

• can anyone explain, what is mean by evidence column in SNIPPY?

  #557 opened a year ago by neelam19051
  1

• Are SNPs quality filtered previous to snippy-core?

  #562 opened a year ago by alanxelena
  0

• Snippy-multi returns 0 SNPs while snippy finds multiple

  #560 opened a year ago by asad-869
  0

• bad ID for snippy-multi tab file

  #559 opened a year ago by medp8144
  0

• vcfuniq: symbol lookup error: lib/libvcflib.so.1: undefined symbol: wavefront_align

  #556 opened a year ago by cpplyqz
  5

• snippy-multi returns 0 SNPs

  #558 opened a year ago by asad-869
  0

• snippy -Loaded 1 sequences totalling 0 bp

  #555 opened a year ago by hooohw
  0

• Unknown option: mask on snippy-clean_full_aln

  #553 opened a year ago by KatyaArnold
  0

• snps.tab file not created

  #552 opened 2 years ago by jennifercalawa
  0

• "Snepff problem because of java version"

  #551 opened 2 years ago by carlosfreytas
  0

• Error: Please supply a reference FASTA/GBK/EMBL file with --reference , even in the presence of reference file

  #547 opened 2 years ago by neelam19051
  1

• Debian and Guix support for snippy

  #550 opened 2 years ago by pjotrp
  3

• snippy-core ignore "snps" of some fragments, although they exists in snps.vcf of individual genome.

  #548 opened 2 years ago by actledge
  1

• freebayes Error: signal 11: when using --targets

  #549 opened 2 years ago by mlarjim
  0