Merge output needs to be fixed for Ingenuity processing

[somalee]

The HugeSeq output for SNPs and indels right now consists of a final merged file containing both the GATK and Samtools SNP/indel calls. However, the way the file is merged right now, the two input files are treated as separate samples i.e. causes it to act like it is just a concatenation of two vcfs from different samples in ingenuity. I believe it's just a matter of fixing the header info. According to our contact at Ingenuity, if GATK's "CombineVariants" was used to combine the vcfs I think there is a way to force it to treat the inputs as coming from the same sample. Can you please look into this? - Submitted on behalf of Rajini R Haraksingh, Satnford