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Can I select which samples of a merged gVCF to use in GenotypeGvcf command line?

Basically what I would like to do is give a selection of sample names to use to GenotypeGvcf so that only a subset of the samples in a merged gVCF file is used. So if I would have a merged gVCF file with sample A, B and C I would like to be able to do

 java -jar GenomeAnalysisTK.jar \
    -T GenotypeGVCFs \
    -R reference.fasta \
     --variant sample1.g.vcf \
     --variant sample2.g.vcf \
    -o output.vcf \
    **--subset A, B**

so that only sample A and B are used. I could not find such a parameter existing, but I may have missed it. Is this possible?


Best Answer


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