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

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8.1 years ago

parisahmadloo2014 • 0

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 • 2.5k views

ADD COMMENT • link updated 6.8 years ago by Biostar 20 • written 8.1 years ago by parisahmadloo2014 • 0

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

ADD REPLY • link 8.1 years ago by Pierre Lindenbaum 161k

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Are you looking for a tool like bcftools ?

ADD REPLY • link 8.1 years ago by iraun 6.2k

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