Why manifest samples are missing from the allele data

Mad4hatter only writes a sample to the allele table when at least one allele remains after DADA2 and post-processing, so samples with no final reads (for example clean negative controls) are expected to be missing.

Usage

samples_missing_from_allele_data(manifest, sample_coverage, allele_data)

Arguments

manifest

Manifest from read_manifest().

sample_coverage

Sample coverage from Mad4hatter.

allele_data

Allele data from Mad4hatter.

Value

Manifest samples (including controls) with no allele data, with reason: either not in the pipeline results at all, or in the results but with no alleles after DADA2 and post-processing.