Merging InDel with SNP position.

[Job van Riet]

Fix the merging of positions with an InDel in one sample and a SNP in another sample. This position will now be filtered entirely instead of the InDel sample having NA.

[Job van Riet]

Added a filtering step prior to loading in the VCF data, using bcftools which removes InDels at multiallelic sites.

bcftools view $vcf --exclude-types indels > SNPs_$vcf