Pisces Suite 5.2.0 Known Issues and Limitations - Illumina/Pisces GitHub Wiki

Known issue: Stitcher multithreading has a bug that can cause it to write corrupt bam files. Do not use the -NumThreads parameter until the next release.

Known compatibility issue: Pisces genome VCF files lack the "GQX" field, making them incompatible with VariantStudio v2.2 and below.