Geraldine Van der Auwera a6f632874b Various documentation improvements ... - Edited intervals merging docs for correctness & clarity - Edited VQSR arg docs and made mode required (+added -mode SNP to VQSR tests) - Moved PaperGenotyper to Toy Walkers to declutter the actually useful docs - Moved GenotypeGVCFs to Variant Discovery category and clarified a few points - Clarified that the -resource argument depends on using the -V:tag format - Clarified how the pcr indel model works - Added caveat for -U ALLOW_N_CIGAR_READS - Added MathJax support for displaying equations in GATKDocs - Updated HC example commands and caveats		2014-07-14 12:03:03 -04:00
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helpTemplates	Various documentation improvements	2014-07-14 12:03:03 -04:00