Menachem Fromer 6984ab0c78 Change ReadBackedPhasing to be VCF4.1 compliant (but instead of using PS tags, it uses HP tags for pairs of diploid haplotype labels). The important point is that it no longer uses the '|' character instead of '/' or flips around the allele order in the genotype. Instead, the HP FORMAT targ is used to mark the haplotype labels with respect to other genotypes for the same sample. Note that this enables the phasing of non-consecutive (but nearby) sites, based on mate pairs, for example. Also, updated the HaplotypeCallerValidation Qscript to perform PhaseByTransmission (if ped file given) and then ReadBackedPhasing		2013-01-08 16:40:32 -05:00
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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	…
java	Change ReadBackedPhasing to be VCF4.1 compliant (but instead of using PS tags, it uses HP tags for pairs of diploid haplotype labels). The important point is that it no longer uses the '|' character instead of '/' or flips around the allele order in the genotype. Instead, the HP FORMAT targ is used to mark the haplotype labels with respect to other genotypes for the same sample. Note that this enables the phasing of non-consecutive (but nearby) sites, based on mate pairs, for example. Also, updated the HaplotypeCallerValidation Qscript to perform PhaseByTransmission (if ped file given) and then ReadBackedPhasing	2013-01-08 16:40:32 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	merge development branchs of log-less HMM and FastGatherer to master	2013-01-06 23:01:58 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00