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The numbers of variants in GATK SV --concordance output

tytolintytolin Member
edited May 2018 in Ask the GATK team

what is the true meaning of SV --concordance?
I have a vcf produced by GATK UG containing 5162953 variants and a vcf generated by samtools which has 244095 variants.
After SV –concordance for these two files, I get a vcf containing 2664909 variants.
I think it seems abnormal.
From the manual of SV, we know that we can “Select all calls made by both myCalls and theirCalls (useful to take a look at what is consistent between two callers)”
Does it mean that I can get those variants which is in both two vcf files?
If it is true, does that mean the vcf I generated from SV –concordance is not correct? or the SV –concordance use other algorithm to do such work?

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