USeq Source Code

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

Source Code Commit Log

Commit	Date
[r193] by monkeymanstan Added code to call Picard's SortSam and MarkDuplicates at start of NBP	2013-12-16 16:22:36	Tree
[r192] by tmosbruger VCFSample: Mark samples with no depth information as no-calls	2013-12-11 18:45:14	Tree
[r191] by biotelerock DefinedRegionDifferentialSeq * Changed the default minimum read count threshold to 20 from 10. This lower number was allowing too many low hit genes into the multiple testing correct and causing the FDRs to be significantly lower than necessary. VCFComparator * Added checks to convert 0\|1 genotypes to 0/1, and 1/0 calls to 0/1; these are needed to standardize the calls and enable genotype matching with the NIST key SamTranscriptomeParser * Bug fix for merging paired alignments where an insertion occurred immediately before the start of the second read	2013-12-10 22:50:48	Tree
[r190] by biotelerock Added modifications to support datasets lacking whole strands, needed for amplicon data.	2013-12-09 22:35:25	Tree
[r189] by biotelerock Added modifications to support datasets lacking whole strands, needed for amplicon data.	2013-12-09 21:30:22	Tree
[r188] by biotelerock Lots of mods to support the processing of methylated datasets where particular chromosomes only have + or - stranded data and not both. This breaks most everything. Ugg.	2013-12-06 23:44:18	Tree
[r187] by biotelerock Added new beta app for annotating vcf variants with splice junction affects.	2013-12-03 22:57:09	Tree
[r186] by tmosbruger Bug Fix	2013-12-03 18:13:50	Tree
[r185] by biotelerock Added ability to set the minimum base read coverage threshold, defaults to 5 alignments	2013-12-02 21:10:53	Tree
[r184] by tmosbruger Added support for David's best practices to TomatoFamer. See 'exome_best'	2013-12-02 15:03:47	Tree

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