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final result

The question is that after running GenotypeGVCF, and getting VCF file then how we can get the result for every sample we have run GenotypeGVCF. I mean if we run haplotyping for 100 samples and getting the gVCF for every sample then at the end of the day after getting the VCF file we want to produce the result for every sample how to produce 100 results for 100 samples?


  • EADGEADG KielMember ✭✭✭

    Hi @meta1360,

    take a look at Select Variants, here a slice from the docs:

     java -jar GenomeAnalysisTK.jar \
       -T SelectVariants \
       -R reference.fasta \
       -V input.vcf \
       -o output.vcf \
       -sn SAMPLE_A_PARC \
       -sn SAMPLE_B_ACTG

    Greets EADG

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