The default parameters for the VariantCaller plugin, specifically for germline exome calls on 540 chips (ampliseq_germline_lowstringency_540_parameters.json), have changed drastically from version 5.8 to version 5.10. For example, ["torrent_variant_caller"]["snp_min_coverage"] has changed from 20 to 35, which I assume will cause VariantCaller version 5.10 to skip variants with low read counts that would have been called in version 5.8. Minimum coverage parameters for MNPs and indels have been similarly increased. Is this documented somewhere?
The default parameters for the VariantCaller plugin, specifically for germline exome calls on 540 chips (ampliseq_germline_lowstringency_540_parameters.json), have changed drastically from version 5.8 to version 5.10. For example, ["torrent_variant_caller"]["snp_min_coverage"] has changed from 20 to 35, which I assume will cause VariantCaller version 5.10 to skip variants with low read counts that would have been called in version 5.8. Minimum coverage parameters for MNPs and indels have been similarly increased. Is this documented somewhere?