Eric Banks 77868d034f Do not allow the use of Ns in reads for graph construction. ... Ns are treated as wildcards in the PairHMM so creating haplotypes with Ns gives them artificial advantages over other ones. This was the cause of at least one FN where there were Ns at a SNP position.		2013-06-11 11:51:26 -04:00
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annotator	Refactor rsID and overlap detection in VariantOverlapAnnotator utility class	2013-06-10 15:51:13 -04:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	Make BQSR calculateIsIndel robust to indel CIGARs are start/end of read	2013-05-31 13:58:37 -04:00
compression/reducereads	Fix error in merging code in HC	2013-05-31 16:29:29 -04:00
diagnostics	Update MD5s and the Diagnose Target scala script	2013-05-13 12:06:17 -04:00
diffengine	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
genotyper	Refactor rsID and overlap detection in VariantOverlapAnnotator utility class	2013-06-10 15:51:13 -04:00
haplotypecaller	Do not allow the use of Ns in reads for graph construction.	2013-06-11 11:51:26 -04:00
indels	Secondary alignments were not handled correctly in IndelRealigner	2013-05-06 19:09:10 -04:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
variantrecalibration	Update MD5s for VQSR header change	2013-04-16 11:45:45 -04:00
variantutils	CombineVariants no longer adds PASS to unfiltered records	2013-05-20 16:53:51 -04:00