Pisces Suite 5.1.6 Known Issues and Limitations - Illumina/Pisces GitHub Wiki

  • Known issue: Stitcher is incompatible with reads for which stitched basecall qualities will exceed 93. For example, if R1 basecall quality is 60 and R2 basecall quality is 33, or R1 basecall quality is 47 and R2 basecall quality is 46. The resulting quality in the stitched read, if it exceeds 93, does not conform to the Sanger format for encoding (see https://en.wikipedia.org/wiki/FASTQ_format#Encoding). For this reason, it is recommended that Stitcher is not run on reads likely to have basecall qualities over 47. Future releases will cap the stitched quality.
  • Known compatibility issue: Pisces genome VCF files lack the "GQX" field, making them incompatible with VariantStudio v2.2 and below.