merging VCF files from different samples and seprating each samples by coloumns · Biostar

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merging VCF files from different samples and seprating each samples by coloumns

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

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updated 9.1 years ago by Biostar

• written 10.4 years ago by parisahmadloo2014 •

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

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written 10.4 years ago by Pierre Lindenbaum

Are you looking for a tool like bcftools ?

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written 10.4 years ago by iraun

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