What is it?
- This QC is applied after reads are aligned to a reference assembly.
bases_dedup_minchecks that the number of bases remaining after removal of (either PCR or optical) duplicate reads is above some minimum number.
bases_dedup_mapped_minchecks that the number of bases remaining after removal of (either PCR or optical) duplicate reads and the removal of unmapped or non-primary alignments is above some minimum number.
- Samples that fail this QC check do not have enough high-quality reads on which to perform further analysis
Possible reasons for failure:
- High rates of PCR or optical duplicates would lead to a small number of bases remaining after the removal of such reads
- High rates of contamination or reads from organisms other than that for which the reference genome was constructed would lead to a small number of bases remaining after removing unmapped or non-primary alignments.
- High duplication rates are typically due to factors involved upstream of data generation such as library preparation or low input samples.