pcingola/SnpSift

Issues

• SnpSift Filter issue

  #90 opened 3 months ago by Am3LieC
  1

• Missing usage documentation on gtfilter

  #88 opened 4 months ago by IdoBar
  1

• SnpSift split outputs only the first chromosome

  #81 opened 2 years ago by kmavrommatis
  6

• can snpsift rename the INFO/TAG？

  #87 opened 8 months ago by litun-fkby
  0

• Adding alphamissense and other annotations from the latest dbNSFP

  #86 opened 10 months ago by ramirobarrantes
  0

• SnpSift gwasCat added vcf header to the end of the vcf file

  #42 opened 3 years ago by hou
  2

• how to filter based on FREQ?

  #83 opened a year ago by chunxuan-hs
  0

• annotate INFO allele specifically

  #48 opened 3 years ago by lozybean
  1

• extract "ANN[*].RANK" from the ANN field

  #82 opened 2 years ago by gcy0115
  0

• Build issue: "SnpSift: Could not resolve dependencies for project"

  #80 opened 2 years ago by kbipinkumar
  1

• CNV error

  #78 opened 2 years ago by weichenyangs
  0

• Help with specific filter syntax

  #77 opened 2 years ago by ohudson1
  0

• Filtering variants with a supporting read in the normal sample

  #76 opened 2 years ago by yoakiyama
  0

• Unable to pass SnpEff output to SnpSift

  #75 opened 2 years ago by rhdolin
  2

• How to deal with conflicting INFO field names

  #73 opened 2 years ago by rhdolin
  1

• annotate parameters

  #74 opened 2 years ago by lmanchon
  0

• "SnpSift.jar annotate -id" and "SnpSift.jar annotate" have the same results

  #72 opened 2 years ago by jiriny
  0

• filter intergenic region structural variants

  #71 opened 2 years ago by prasundutta87
  0

• dbNSFP not annotating entries

  #70 opened 2 years ago by ji575
  1

• INTERVAL header missing

  #69 opened 3 years ago by Talya-dor
  0

• Mismatch between LICENSE.md and pom.xml concerning the license

  #68 opened 3 years ago by pgrt
  0

• junit scope should be "test" in pom.xml

  #67 opened 3 years ago by pgrt
  0

• dbSNP not found

  #66 opened 3 years ago by GENEDECODERS
  0

• Log4j vulnerability

  #64 opened 3 years ago by sandra-selfdecode
  0

• SnpSift Extract Fields: GT does not match Allele

  #63 opened 3 years ago by saphiecor
  0

• Dashes in variant names

  #62 opened 3 years ago by ChadMatsalla
  0

• SnpSift in multiallelic variants

  #61 opened 3 years ago by rogeriobioinfo
  0

• line 1:11 no viable alternative at input '[*].GENE:'

  #53 opened 3 years ago by AroobAlhumaidy
  3

• Missing 'chr' columns in dbNSFP file

  #60 opened 3 years ago by shangyf-stu
  1

• dbNSFP annotation inconsistent and incorrect when caching

  #45 opened 3 years ago by yarongolan
  0

• SnpSift extractFields ANN[0].RANK

  #46 opened 3 years ago by zzupmc
  2

• Preserving '.' in Float fields in ExtractFields

  #49 opened 3 years ago by bingxiao
  0

• No white-space, semi-colons, or equals-signs are permitted in INFO field values

  #50 opened 3 years ago by rrdavis77
  0

• Add support for dbscSNV

  #35 opened 3 years ago by pcingola
  0

• dbNSFP: Incorrect VCF header NUMBER

  #36 opened 3 years ago by pcingola
  0

• FILTER for '*' or '?' constraint for more than 1 variable not supported

  #38 opened 3 years ago by mitochon
  1

• SNPSIFT extractFields

  #43 opened 3 years ago by rtemanni
  2

• Interpreting results of java -jar SnpSift.jar concordance

  #51 opened 3 years ago by montenegrina
  2

• How to read this SNPEff output

  #55 opened 3 years ago by SimoneFromThePlantLab
  0

• How to escape special characters in SnpSift filter query string?

  #56 opened 3 years ago by marcora
  4

• how to download dbSNP142.vcf file?

  #59 opened 3 years ago
  1

• SnpSift CaseControl - statistics clarity

  #57 opened 4 years ago by dtlyfoung
  1

• dbNSFPv4.1a database does not index using tabix

  #54 opened 4 years ago by kgandh2
  1

• SnpSift annMem not working any more

  #40 opened 7 years ago by nsoranzo
  1

• SnpSift vcfCheck broken in v4.3o

  #41 opened 7 years ago by nsoranzo
  1

• Create new VCF file index (plain VCf files)

  #30 opened 9 years ago by pcingola
  1

• Convert VCF index to a generic interval annotation

  #31 opened 9 years ago by pcingola
  1

• SnpSift grfilter: Genotype missing should be './.' instead of '.'

  #32 opened 9 years ago by pcingola
  1

• escaping () in extractFields

  #29 opened 9 years ago by asalomatov
  3

• ExtractFields does not recognize GERP++ fields in VCF header

  #27 opened 9 years ago by mlist
  2