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  1. java
  2. -jar GenomeAnalysisTK.jar
  3. -T ContEst
  4. -R reference.fasta
  5. -I:eval tumor.bam
  6. -I:genotype normal.bam
  7. --popfile populationAlleleFrequencies.vcf
  8. -L populationSites.interval_list
  9. [-L targets.interval_list]
  10. -isr INTERSECTION
  11. -o output.txt
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