- Significantly improved our handling of samples sequenced using amplicon kits.
- Updated third party pipeline tools.
We have reorganized our amplicon-preprocessing step so it now uses samtools ampliconclip to clip primer sequences. In addition, we now process amplicon bam files more aggressively to remove reads with quality issues and produce a cleaner alignment. This change is expected to result in an increase in the number of true positive calls near the edges of amplicons and a decrease in the number of false positive calls elsewhere.
The changes will only affect samples sequenced using amplicon kits and we do not expect significant changes to capture kit samples.
Third party Software Updates
We have updated several of our pipeline software tools. You can always see what versions of the various tools were used in your analysis’ QC report.
As always, we hope these changes reflect our company mission statement “To enable anyone to find, share, use the most comprehensive human genome data - and to collaborate to improve health and lives around the world.” and we continue to value your feedback so that we can continue to improve in all areas of development.
Further Information and Support
As ever we hope you find these changes and improvements helpful, we’d love to hear any suggestions you may have, support is available as usual from email@example.com
- The VarSome Team