For the snps to create combine snps and filtered indels, now using a VCF with just snps instead of vcf with snps plus unfiltered indels.
For the snps to create combine snps and filtered indels, now using a VCF with just snps instead of vcf with snps plus unfiltered indels.

git-svn-id: 4561c0a8f080806b19201efb9525134c00b76d40@5904 348d0f76-0448-11de-a6fe-93d51630548a

iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable