STAR 2.6.0c 2018/05/10

Fixed bugs in merging mates (--peOverlap*) and WASP filtering algorithms. Please see CHANGES and RELEASEnotes from 2.6.0a below.

STAR 2.6.0b 2018/05/02

Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.6.0a below.

Merging and mapping of overlapping paired-end reads with new options --peOverlapNbasesMin and --peOverlapMMp. The developmment of this algorithm was supported by Illumina, Inc. Many thanks to June Snedecor, Xiao Chen, and Felix Schlesinger for their extensive help in developing this feature.
--varVCFfile option to input variant VCF file.
New SAM attributes in the --outSAMattributes, vG, vA, and vW to report variants overlapping alignments.
--waspOutputMode option for filtering allele specific alignments. This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061–1063 (2015), https://www.nature.com/articles/nmeth.3582 . Many thanks to Bryce van de Geijn for fruitful discussions.
Detection of multimapping chimeras, with new options --chimMultimapNmax, --chimMultimapScoreRange and --chimNonchimScoreDropMin . Many thanks to Brian Haas for testing and feedback.

--alignInsertionFlush option which defines how to flush ambiguous insertion positions: None: old method, insertions are not flushed; Right: insertions are flushed to the right.
--outSAMtlen option to select the calculation method for the TLEN field in the SAM/BAM files.
--outBAMsortingBinsN option to control the number of sorting bins. Increasing this number reduces the amount of RAM required for sorting.