While benchmarking GIAB data with nf-core/sarek (DeepVariant and HaplotypeCaller), we observed several false positives occurring at homopolymer boundaries. GIAB confirmed this is a common source of errors and suggested we ask here about best practices. Do you have recommended filtering strategies within Sarek (or downstream QC) to handle homopolymer-related FPs for DV and HC? Example variants: • chr1:115725557 GAAA>G • chr10:87960876 C>CT • chr3:10152060 CA>C • chr9:132897613 G>GAA Thanks in advance for any guidance.

Hi, @Mohammad Khatib! Slack uses channels to organise discussions. Press the

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more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Phil Ewels for help.

#CGFUX04HZ is your best bet for this question :)

Thanks!