The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.

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


Sign In or Register to comment.