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• help with the acount of the total number of variants fron vcf file
  i have a vcf file and now how can i proceed to have the number ofsingle nucleotide variants, the ...
• VCF file samples not called
  I'm trying to identify polymorphisms in three samples. When I get the VCF file there are many var...
• DBSNP, Variant Caller
  I have a VCF file from FreeBayes Variant caller. However I want VCF file to have dbSNP (rsID). T...
• Loss of original VCF file; therefore in Galaxy, can I use VCF manipulation on an excel file (originally converted from VCF format)
  I have inherited a project where the original VCF files were lost. I have the excel files derived...
• Filter Varscan VCF
  Hello, I have a VCF file obtained from the Varscan tool. I want to filter the variants based on ...
• getting number of SNPs, insertion/deletion from VCF with VCFfilter
  Hello, I am trying to extract from a VCF file the number of SNPs: Single nucleotide variants , I...
• Hello help for annovar..
  I need some help.. I have this . Using your resulting VCF determine 1) the number of single nucle...
• ANNOVAR annotate cuts short the VCF file ?
  I uploaded a standard VCF that contains 57651 lines (or 57471 lines variant data) and ran it with...
• How can I annotate a vcf file created with Freebayes with rs#
  Hi All, I have a vcf file created in freebayes (v.0.0.2), and I would like to annotate the file...
• How to separate SNPs from other variant types in Galaxy?
  I have a VCF file with all the called variants. I want to keep just the SNPs. This is achievable ...
• How to classify the variants into different groups?
  Hello, This is my first time using galaxy. I ran Free Bayes to detect the variants of a data set ...
• empty QUAL filed in Naive Variant caller vcf output
  Hi, The QUAL field in vcf output of Naive Variant Caller is empty for all the variants. Any reas...
• Conversion of a .vcf (variant control format) to a .maf (mutation annotation file)
  Hello, Is there a galaxy package which will convert a .vcf to a .maf (mutation annotation file)?...
• Filtering Variants using Snpsift filter and SnpEff
  Hi, I have a bunch of variants in .VCF file which I got through the unified genotyper tool. Now ...
• bam to VCF
  Hi, I am trying to get all the variants from sequencing data. From fastaq, I got BAM files. Then...
• What to write in "Using reference genome" and "Annotation Regions"sections ?
  Hey, I am trying to use GATK through Galaxy and trying to call variants from my vcf file. "Selec...
• VCF output from Mpileup tool
  Hi everyboy, I am trying to call SNP using the SAM Tools → mpileup in Galaxy. Since the input ...
• GEMNI doesn't recognize hg19 VCF file!
  I am trying to import my hg19 variant call file, but on GEMNI tab, it appears it doesn't recogniz...