diff --git a/ingest/config/nextclade_field_map.tsv b/ingest/config/nextclade_field_map.tsv deleted file mode 100644 index 513b0fd..0000000 --- a/ingest/config/nextclade_field_map.tsv +++ /dev/null @@ -1,18 +0,0 @@ -# TSV file that is a mapping of column names for Nextclade output TSV -# The first column should be the original column name of the Nextclade TSV -# The second column should be the new column name to use in the final metadata TSV -# Nextclade can have pathogen specific output columns so make sure to check which -# columns would be useful for your downstream phylogenetic analysis. -seqName seqName -clade clade -lineage lineage -coverage coverage -totalMissing missing_data -totalSubstitutions divergence -totalNonACGTNs nonACGTN -qc.missingData.status QC_missing_data -qc.mixedSites.status QC_mixed_sites -qc.privateMutations.status QC_rare_mutations -qc.frameShifts.status QC_frame_shifts -qc.stopCodons.status QC_stop_codons -frameShifts frame_shifts