Usage of import-to-loculus
Command
The import-to-loculus
command is used to convert BAM alignments to SILO format and optionally upload the results to SILO.
Important Note
Before using the import-to-loculus
command, ensure that primers have been trimmed off from the input BAM file. This means that either soft-clippings or hard-clippings must be applied to the input file to remove primer sequences.
Command Overview
The basic usage of the command is as follows:
sr2silo import-to-loculus \
--input-file INPUT.bam \
--sample-id SAMPLE_ID \
--batch-id BATCH_ID \
--timeline-file TIMELINE.tsv \
--primer-file PRIMERS.yaml \
--output-fp OUTPUT.ndjson \
--reference sars-cov-2
Required Arguments
--input-file, -i
: Path to the input BAM alignment file.--sample-id, -s
: Sample ID to use for metadata.--batch-id, -b
: Batch ID to use for metadata.--timeline-file, -t
: Path to the timeline metadata file.--primer-file, -p
: Path to the primers configuration file.--output-fp, -o
: Path for the output file (will be auto-suffixed with.ndjson.zst
).
Optional Arguments
--reference, -r
: The nucleotide/amino acid reference from the resources folder. Default issars-cov-2
.--upload/--no-upload
: Whether to upload and submit to SILO. Default is--no-upload
.--skip-merge/--no-skip-merge
: Whether to skip merging of paired-end reads. Default is--no-skip-merge
.
Example Usage
sr2silo import-to-loculus \
--input-file ./data/sample/alignments/REF_aln_trim.bam \
--sample-id "A1_05_2024_10_08" \
--batch-id "20241024_2411515907" \
--timeline-file ./data/timeline.tsv \
--primer-file ./data/primers.yaml \
--output-fp ./results/output.ndjson \
--reference sars-cov-2
To also upload the results to SILO, add the --upload
flag: