Index

Symbols

--a_eps freyja-demix command line option --adapt freyja-demix command line option --annot freyja-covariants command line option freyja-get-lineage-def command line option freyja-variants command line option --autoadapt freyja-boot command line option freyja-demix command line option --barcodes freyja-boot command line option freyja-demix command line option freyja-get-lineage-def command line option --bodyColor freyja-dash command line option --bootseed freyja-boot command line option --boxplot freyja-boot command line option --buildlocal freyja-update command line option --config freyja-dash command line option freyja-plot command line option freyja-relgrowthrate command line option --confirmedonly freyja-boot command line option freyja-demix command line option --covcut freyja-demix command line option --days freyja-dash command line option freyja-relgrowthrate command line option --depthcutoff freyja-boot command line option freyja-demix command line option --depths freyja-variants command line option --eps freyja-boot command line option freyja-demix command line option --ext freyja-aggregate command line option --grthresh freyja-dash command line option freyja-relgrowthrate command line option --headerColor freyja-dash command line option --interval freyja-plot command line option --keep_plot_files freyja-dash command line option --lineages freyja-plot command line option --lineageyml freyja-boot command line option freyja-dash command line option freyja-demix command line option freyja-plot command line option freyja-relgrowthrate command line option --meta freyja-boot command line option freyja-demix command line option --min_count freyja-covariants command line option --min_mutations freyja-plot-covariants command line option --min_quality freyja-covariants command line option --mincov freyja-dash command line option freyja-plot command line option freyja-relgrowthrate command line option --minq freyja-variants command line option --nb freyja-boot command line option --nboots freyja-dash command line option freyja-relgrowthrate command line option --noncl freyja-barcode-build command line option freyja-update command line option

--nt freyja-boot command line option --nt_muts freyja-plot-covariants command line option --num_clusters freyja-plot-covariants command line option --outdir freyja-barcode-build command line option freyja-update command line option --output freyja-aggregate command line option freyja-covariants command line option freyja-dash command line option freyja-demix command line option freyja-extract command line option freyja-filter command line option freyja-get-lineage-def command line option freyja-plot command line option freyja-plot-covariants command line option freyja-relgrowthrate command line option --output_base freyja-boot command line option --pathogen freyja-barcode-build command line option freyja-boot command line option freyja-dash command line option freyja-demix command line option freyja-plot command line option freyja-relgrowthrate command line option freyja-update command line option --pb freyja-barcode-build command line option --rawboots freyja-boot command line option --ref freyja-get-lineage-def command line option freyja-variants command line option --ref-genome freyja-covariants command line option --refname freyja-variants command line option --region_of_interest freyja-demix command line option --relaxedmrca freyja-boot command line option freyja-demix command line option --relaxedthresh freyja-boot command line option freyja-demix command line option --same_read freyja-extract command line option --scale_by_viral_load freyja-dash command line option freyja-relgrowthrate command line option --serial_interval freyja-dash command line option freyja-relgrowthrate command line option --solver freyja-boot command line option freyja-demix command line option --sort_by freyja-covariants command line option --spans_region freyja-covariants command line option --threads freyja-covariants command line option --thresh freyja-dash command line option freyja-plot command line option freyja-relgrowthrate command line option --times freyja-plot command line option --variants freyja-variants command line option --varthresh freyja-variants command line option --version freyja-demix command line option --vmax freyja-plot-covariants command line option --vmin freyja-plot-covariants command line option --windowsize freyja-plot command line option --writegrouped freyja-plot command line option

A

AGG_RESULTS freyja-dash command line option freyja-plot command line option freyja-relgrowthrate command line option

B

BAMFILE freyja-variants command line option

C

COVARIANTS freyja-plot-covariants command line option

D

DEPTHS freyja-boot command line option freyja-demix command line option

F

freyja-aggregate command line option --ext --output RESULTS freyja-barcode-build command line option --noncl --outdir --pathogen --pb freyja-boot command line option --autoadapt --barcodes --bootseed --boxplot --confirmedonly --depthcutoff --eps --lineageyml --meta --nb --nt --output_base --pathogen --rawboots --relaxedmrca --relaxedthresh --solver DEPTHS VARIANTS freyja-covariants command line option --annot --min_count --min_quality --output --ref-genome --sort_by --spans_region --threads INPUT_BAM MAX_SITE MIN_SITE freyja-dash command line option --bodyColor --config --days --grthresh --headerColor --keep_plot_files --lineageyml --mincov --nboots --output --pathogen --scale_by_viral_load --serial_interval --thresh AGG_RESULTS INTRO METADATA TITLE freyja-demix command line option --a_eps --adapt --autoadapt --barcodes --confirmedonly --covcut --depthcutoff --eps --lineageyml --meta --output --pathogen --region_of_interest --relaxedmrca --relaxedthresh --solver --version DEPTHS VARIANTS

freyja-extract command line option --output --same_read INPUT_BAM QUERY_MUTATIONS freyja-filter command line option --output INPUT_BAM MAX_SITE MIN_SITE QUERY_MUTATIONS freyja-get-lineage-def command line option --annot --barcodes --output --ref LINEAGE freyja-plot command line option --config --interval --lineages --lineageyml --mincov --output --pathogen --thresh --times --windowsize --writegrouped AGG_RESULTS freyja-plot-covariants command line option --min_mutations --nt_muts --num_clusters --output --vmax --vmin COVARIANTS freyja-relgrowthrate command line option --config --days --grthresh --lineageyml --mincov --nboots --output --pathogen --scale_by_viral_load --serial_interval --thresh AGG_RESULTS METADATA freyja-update command line option --buildlocal --noncl --outdir --pathogen freyja-variants command line option --annot --depths --minq --ref --refname --variants --varthresh BAMFILE

I

INPUT_BAM freyja-covariants command line option freyja-extract command line option freyja-filter command line option

INTRO freyja-dash command line option

L

LINEAGE freyja-get-lineage-def command line option

M

MAX_SITE freyja-covariants command line option freyja-filter command line option METADATA freyja-dash command line option freyja-relgrowthrate command line option

MIN_SITE freyja-covariants command line option freyja-filter command line option

Q

QUERY_MUTATIONS freyja-extract command line option freyja-filter command line option

R

RESULTS freyja-aggregate command line option

T

TITLE freyja-dash command line option

V

VARIANTS freyja-boot command line option freyja-demix command line option