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Compare Cohort 1 and Cohort 2: Make file with SNPs that are only in Cohort 1, not in Cohort 2

myoglumyoglu Member Posts: 39

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!



Best Answer


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