v5.3.0.0

This build is not an official illumina release, but a link to a more Linux-friendly personal fork. Source, here: (https://github.com/tamsen/Pisces/) . This version does not require dotnet core to be installed as a pre-req to running Pisces, and supports development & debugging on Linux OS.

get binaries at: https://github.com/tamsen/Pisces/releases/tag/v5.3.0.0

For more details see
https://github.com/tamsen/Pisces/blob/master/README.md
https://github.com/tamsen/Pisces/wiki

v5.2.10.49

Major Changes:

• Introducing GeminiMulti as a mate-aware indel realigner. This combines the best of Hygea (realigner) and Stitcher (the read stitcher), using a read's mate to inform realignment (if a mate is available). With no mate, it falls back to just doing indel realignment. Gemini is also smoking fast. Gwenn Berry is the lead developer for Gemini. Note that Gemini is very new, and may be hardened/refactored in future releases. When using Gemini with Pisces, please set -UseStitchedXD true.

• Introducing AdaptiveGenotyper as a new alternative to the simplistic threshold-based germline genotyping model originally in Pisces. To use AdaptiveGenotyper, take a normal BAM from a germline sample. Call with Pisces in somatic, uncrushed VCF mode (in order to report all alleles present, including noise). AdaptiveGenotyper will then adaptively build up three-component (or four-component) binomial mixture models as appropriate for a diploid sample, and re-genotype based on those models. Sidney Kuo is the lead developer for the AdaptiveGenotyper. Note that AdaptiveGenotyper is very new, and may be hardened/refactored in future releases.

Minor Fixes:

• VennVcf is no longer so finicky about chr names.
• Pisces allows non-anchored indels

v5.2.9.122

Minor upgrades:

• Pisces has a new algorithm, the "Tunable Ambiguity Calculator for Tiled Insertion Coverage" (TACTIC) , which allows for more accurate frequency calculations for insertions spanning tiled read boundaries. This offsets common aligner error modes in repeat regions. For example, when a detected sequence might match both the reference and a discovered insertion, this algorithm may allow support to be given to the insertion over the reference.

• Pisces has a new nocall filter. The "NC" filter tag is now automatically added to variants in regions where more than 60% of the bases are no calls ("N"). The point of this filter is to alert the user to regions of the genome where significant portions of the basecalls are unreliable. Variant calls (and alignments) in these regions are suspect.

• the RMxN filter default value is now "5,9,0.35," changed from "5,9,0.20". While our general philosophy with filter values is to expose them and help our users find what works best for them, the 35% setting has been consistently optimal for us on a broad range of data sets.

v5.2.7.47

• Argument parsing refactor and major face lift
• Beta release of Indel Realigner "Hygea" (warning. work in progress!)
• Release of handy tool "CreateGenomeSizeFile"
• Depracated options:
  RepeatFilter -> use RMxN for better results
  BamFolder -> use Bam for the same effect

v5.2.5.20

Release of latest Pisces suite. Now on .net core 2.0. Should resolve some configuration issues with .net core 1.0.

v5.2.0.1

Release of latest Pisces suite. First .net core release.

v5.1.6.54

Release of new Pisces version, along with new components Stitcher and Scylla

v5.1.3.60

v5.1.3.60