Hello to all I am using snap software to perform gene prediction. I have already generated the necessary .hmm database, and now I want to …

Hi, I have a vcf file of somatic variants from Varscan2. I tried annotating it with Variant Effect Predictor and snpEff. The online version of …

Hi all, does anyone know about a tool that can phase the variants produced by varscan? I have run varscan in trio mode (for father,mother …

I have some VarScan generated TAB format files (default format) that I want to convert into VCF for IGV visuzaliation. I don't have the source …

<p>I have vcf output from bayesfree and want to convert vcf output to pileup format which will be taken as input for popoolation2. Any script …

Hi, Does anybody know of any script/tool which could convert a MAF file to VCF? https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification?showChildren=false Thanks, Tinu

<p>Dear All,</p> <p>Is there any script available that will help me to convert the VarScan output in .txt format to .vcf format which I can …

<p>The mutation call output of MuTect from Broad is not a standard format that can be loaded into IGV. Does anyone know any tool that …

<p>Hello, I want to do a BLAT alignment on the SNPs I got in my analysis. My VarScan output is in vcf format. Any hints …

I have illumina paired-end reads mapped to reference genome using bowtie and created mpileup using samtools and from mpileup identified SNPs using variant caller (varscan). …