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• 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...
• 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 ...
• Suggestions for variant callers/ problem with BCF view
  Samtools mpileup only outputs genotypes fields for samples when a BCF output is selected. The BCF...
• variants intersect with dbSNP
  Hello, I have a VCF file and I would like only keep variants which are in dbsnp_135.hg19.vcf. H...
• Running FreeBayes to a collection of BAM files individually
  Actually, the FreeBayes variant calling tool generates one VCF file for "all" BAM files selected ...
• DBSNP, Variant Caller
  I have a VCF file from FreeBayes Variant caller. However I want VCF file to have dbSNP (rsID). T...
• Correct way of merging samples for father, mother, child trio variant calling
  I am new to NGS data analysis and I'm working in a multiple-sample variant calling workflow. I ha...
• Filter Varscan VCF
  Hello, I have a VCF file obtained from the Varscan tool. I want to filter the variants based on ...
• How to add flanking sequences to SNPs from vcf files
  Hej, I posted this question in Biostars nad would like to shift this post here to biostars galax...
• 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...
• Mpile up output
  Hi  I am using Mpileup using SAM tools version 1.2+htslib-1.2.1 to generate variants. The tool w...
• VCF break create multi tool
  I want to break a multi vcf file in to individual file. When i execute my query it will create a ...
• Creating a Workflow for Variant Detection for 200 samples
  I have posted this question before and did not receive any responses. Let me try to articulate th...
• Hello help for annovar..
  I need some help.. I have this . Using your resulting VCF determine 1) the number of single nucle...
• 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...
• 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...