Compare Cohort 1 and Cohort 2: Make file with SNPs that are only in Cohort 1, not in Cohort 2
Posted in Ask the GATK team | Last updated on


Comments (2)

Hi! The title says it all. Im trying to narrow down my vcf. Which tools is good to answer this question?

I have tried this:

java -Xmx4g -jar GenomeAnalysisTK.jar \ -R genome.fa \ --filter_reads_with_N_cigar \ -T CombineVariants \ -V:COHORT1 path \ -V:COHORT2 path \ --filteredAreUncalled \ -o path

But the output seams incomprehensibly massive!

Thanks!


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