gatk-sv
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Tabix crashing in single sample pipeline with long sample ID
Tabix will crash if the resulting index filename is longer than 255 characters. This was observed in the ResetFilter
task of the single sample pipeline:
tbx_index_build failed: sample_id.filter_by_ref_panel.reset_HIGH_SR_BACKGROUND_filter.reset_BOTHSIDES_SUPPORT_filter.reset_PESR_GT_OVERDISPERSION_filter.sample_qc.vcf.gz
where sample_id
was too long. We should document this limitation (which would also apply to batch/cohort names, which are also used in filenames) and modify the single sample pipeline to avoid verbose filenames.