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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

fastest way of getting total number of variants in VCF via picard?

What is the fastest way of getting the total number of variants in a VCF file? (using picard-tools-1.119, via SplitVcfs.jar.)

So far the fastest way I could have done it was this:

private static int getNumVariants(VCFFileReader reader) {
int totalVariants = 0;
final CloseableIterator iterator = reader.iterator();
while (iterator.hasNext()) {; totalVariants++; }

  return totalVariants;


  • but this appears to iterate through the entire VCF file which for large files seems very inefficient...

I am thinking that there must be a faster way. After all, the number of variants is simply:
total number of lines in file - number of lines in header?

Any way to get this?




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