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How to split a multi-sample VCF file using SelectVariant?

luongjeluongje Member
edited September 2015 in Ask the GATK team

Hello gatk forums,

Novice gatk user here. I have a VCF file with 200 samples. I am currently trying to split/subset the VCF file such that I am only looking at individual samples. Below is my command line input and the error message I am getting.

java -jar /my/path/GenomeAnalysisTK.jar \ -T SelectVariants \ -R chr22.fa \ -V original.vcf \ -o indiv.vcf \ -sn D66001

Bad input: Samples entered on command line (through -sf or -sn) that are not present in the VCF.

I am sure that my sample is present. What am I doing wrong? Is there an easier way of subsetting a VCF file by sample?



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