-- ArrayList are List where possible
-- states refactored into VariantStratifier base class (reduces many lines of duplicate code)
-- Added VariantType stratification that partitions report by VariantContext.Type
Updates for HybridSelectionPipeline:
- Use VQSR on SNPs for projects using bait set whole_exome_agilent_1 and applying cut at 98.5.
- If a whole_exome_agilent_1 project has less than 50 samples also mixing in 1000G samples to reach VQSR thresholds.
- Updated SNP hard filters based on analysis done with ebanks to approximate VQSR results on small target batches.
- Removed GSA_PRODUCTION_ONLY flag from indel caller.
- Updated indel hard filters based on delangel's analysis.
- Updated HybridSelectionPipelineTest to use HARD SNP filters only, for now.
Found this neat little walker Kiran wrote stashed in the private tree. Very useful. Generalized it a bit, added GATKDocs and moved it to public. I might include it as a QC step on the pacbio processing pipeline.
* generalize it so it works with non pair ended reads.
* generalize it to work with no read group information
* getRefCoordSoftUnclippedEnd was not resetting the shift when hitting insertions. Fixed.
* getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd was returning the wrong read coordinate position. Fixed.
The clipper could leave an insertion or deletion as the start or end of a read after hardclipping a read if the element adjacent to the clipping point was an indel. Fixed.
Read clipper now identifies and clips even if the requested coordinate is outside the alignment but the read contains soft clipped bases in that region.
* When hard clipping a read that had insertions in it, the insertion was being added to the cigar string's hard clip element. This way, the old UnclippedStart() was being modified and so was the calculation of the new AlignmentStart(). Fixed it by subtracting the number of insertions clipped from the total number of hard clipped bases.
* Walker was sending read instead of filtered read when deleting a read that contains only Q2 bases
* Sliding the window was causing reads that started on the new start position to be entirely clipped.
-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
-- Useful if you want to have a parameter like MAX_RECORDS that wants the walker to stop after some number of map calls without having to resort to the old System.exit() call directly.
Reads that were not hard clipped for the variable site no longer show up in output file
Walker now uses unclippedStart of Read to determine position in the sliding Window
Guillermo del Angel
Mark DePristo
Christopher Hartl
Eric Banks
Khalid Shakir
Mauricio Carneiro
Ryan Poplin
Roger Zurawicki