Released on: 6/7/2016 12:55PM
Released by: Kurt Heilman

The most recent version of the HSQutils software user's guide and other information on
the HEAT-Seq product family can be found at the following location:
sequencing.roche.com/heat-seq

This version is identical to the internal version 0.11.

Known issues with HSQutils version 1.0 to be fixed in the next release:

• A known bug exists which may result in a fatal error during the duplicate removal step. To avoid or resolve this error, it is recommend to always sort the BAM file before providing it to HSQutils dedup using a tool such as SAMtools sort or Picard SortSam.
• A second known bug exists that may cause a BAM file validation error for some software tools (e.g. CLC Genomics Workbench). The error occurs for BAM records where an insertion appears between the expected primer sequence and the expected target sequence (usually due to sequencing error), causing a mismatch in length between the query sequence and the CIGAR string. To avoid this issue if it arises please follow the workaround described in the README.txt file included in hsqutils_v1_0.zip. A sample insertion which occurs between the expected primer sequence and the expected target sequence will not be reported when using the workaround even though it is present in the reads. Insertions elsewhere in the target sequence and SNVs throughout the target sequence are unaffected.

Bug Fixes:
NONE

Features:
NONE