Auto-generated from fgumi command definitions.
| Command | Description |
|---|
fastq | Convert BAM to FASTQ format |
zipper | Zip unmapped BAM with aligned BAM |
sort | Sort BAM file by coordinate, queryname, or template-coordinate |
merge | Merge pre-sorted BAM files into a single sorted BAM |
| Command | Description |
|---|
simplex | Call simplex consensus sequences from UMI-grouped reads |
duplex | Call duplex consensus sequences from UMI-grouped reads |
codec | Call CODEC consensus reads from grouped BAM |
| Command | Description |
|---|
dedup | Mark or remove PCR duplicates using UMI information |
| Command | Description |
|---|
group | Group reads by UMI to identify reads from the same original molecule |
| Command | Description |
|---|
filter | Filter consensus reads based on quality metrics |
clip | Clip overlapping reads in BAM files |
duplex-metrics | Collect QC metrics for duplex consensus reads |
review | Extract data to review variant calls from consensus reads |
simplex-metrics | Collect QC metrics for simplex sequencing data |
| Command | Description |
|---|
extract | Extract UMIs from FASTQ and create unmapped BAM |
correct | Correct UMIs in a BAM file to a fixed set of UMIs |
| Command | Description |
|---|
downsample | Downsample BAM by UMI family using streaming |