WHAT IT DOES

Predictions of SNPs from Varscan2, GATK and Freebayes are consolidated into a single call-set following a simple majority consensus rule. Variants identified by at least two methods are incorporated into a final “high confidence” call set.Singleton variants predicted by only one method are considered less reliable and are included in a low quality call-set.

The final output consists in two VCF files:

-SNPs common to at least 2 methods

-Singleton SNPs obtained from a single method