Question: merging VCF files from different samples and seprating each samples by coloumns
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gravatar for parisahmadloo2014
5.0 years ago by
parisahmadloo20140 wrote:

Hi, I have question about how to merge different vcf files as well as separating each sample in the final out put. first i combine 96 samples using java -jar GenomeAnalysisTK.jar \ -T CombineVariants \ -R reference.fasta \ --variant input1.vcf \ --variant input2.vcf \ -o output.vcf \ -genotypeMergeOptions UNIQUIFY then i used annovar for annotation , but at last all variants pooled together and the samples are not separated.

Can i ask how to solve it? Thank you. Parisa

next-gen genome • 2.0k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 5.0 years ago by parisahmadloo20140

please, show us the line starting with "#CHROM" in input1.vcf and input2.vcf

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Pierre Lindenbaum134k

Are you looking for a tool like bcftools ?

ADD REPLYlink written 5.0 years ago by iraun3.8k
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