Ryan Poplin 2e486d83e2 Updating HaplotypeCaller docs and expanding integration tests.		2012-07-23 10:05:42 -04:00
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bqsr	Total rewrite of the isGATKLite() functionality with help of Khalid/David. PluginManager was not working for us.	2012-07-17 15:11:03 -04:00
compression/reducereads	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
genotyper	a) Use new method to check for GATK Like, b) minor improvements to indel pool caller (more to come): brain-dead, quick way to limit number of alt alleles to genotype. We can't process too many alt alleles because of the combinatorial explosion of GL values with high ploidy, and some STR validation targets had up to 12 alt alleles, resulting of GL vectors of > 1e8 elements. Can't use pileup elements since typically not many alleles will be in one pileup, and different alleles will appear in different samples, TBD a nicer solution. c) Commit to posterity scala script for large scale validation calling, still work in progress	2012-07-19 10:24:08 -04:00
haplotypecaller	Updating HaplotypeCaller docs and expanding integration tests.	2012-07-23 10:05:42 -04:00