The functions that need to be added :-

1.) mergevcf using pegasus

How does it need to be done :-

1.) Run combine GVCF on each chromosome of all the vcfs

2.) Once all the chromosomes have been generated run genotype gvcf's on them

3.) Once GenotypeGVCFs have been run on all the chromosomes combine them using combine variants

4.) Add further steps of downstream analysis like SNPeff,visualization and Genomestrip on them and try to make them work