Implement support for indexing VCF files from the targeted genotyping
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
|Priority:||major||Milestone:||Variant Search v1.2|
See Reggie ticket #1323. The VCF files should be more or less compatible with the existing once from the regular variant calling. But there are some differences:
- Each VariantCall may have multiple VCF files from targeted genotyping. The should all be indexed in the same index.
- The AF (Allele frequency) and VD (Variant Depth) fields are not added by the HaplotypeCaller, but they can be calculated from the AD and DP fields.
- The VCF files also contain results for homozygous genotypes. They should be indexed since it may be useful to query everything, but some functions and information need to be changed since they are not all variants.