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2015

05 May 2015 new tools available in Galaxy

We are pleased to announce new tool integrations for Variant analysis in our Galaxy server:

section Freebayes

  • FreeBayes (0.9.20) - bayesian genetic variant detector
  • BamLeftAlign - indels in BAM datasets

 section Vcflib tool suite

  •  VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file
  • VCFselectsamples: Select samples from a VCF dataset
  • VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio
  • VCFdistance: Calculate distance to the nearest variant
  • VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset
  • VCFcombine: Combine multiple VCF datasets
  • VCFflatten: Removes multi-allelic sites by picking the most common alternate
  • VCF-VCFintersect: Intersect two VCF datasets
  • VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines
  • VCFcheck: Verify that the reference allele matches the reference genome
  • VCFrandomSample: Randomly sample sites from VCF dataset
  • VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles
  • VCFgenotypes: Convert numerical representation of genotypes to allelic
  • VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset
  • VCFfilter: filter VCF data in a variety of attributes
  • VCFannotate: Intersect VCF records with BED annotations
  • VCFprimers: Extract flanking sequences for each VCF record
  • VCFsort: Sort VCF dataset by coordinate
  • VCF-BEDintersect: Intersect VCF and BED datasets
  • VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record
  • VCFleftAlign: Left-align indels and complex variants in VCF dataset
  • VCFtoTab-delimited: Convert VCF data into TAB-delimited format
  • VCFcommonSamples: Output records belonging to samples common between two datasets

 

 For any questions or bug reports, please contact us at: urgi-support@versailles.inra.fr
 
 Thank you for using URGI Galaxy: https://urgi.versailles.inra.fr/galaxy2

Update: 01 Jul 2015
Creation date: 05 May 2015