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Commands: genotype
Brice Letcher edited this page Apr 28, 2020
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This command annotates a PRG built by gramtools build with coverage information, genotypes the PRG and infers a personalised reference genome.
The personalised reference is a single (haploid) path through the PRG representing the closest mosaic to your sample in the graph.
It can then be used as a substrate for variant discovery.
gramtools genotype -i ./gram -o ./run --reads ./reads
| parameter | description |
|---|---|
-i |
build command output directory |
-o |
output dir: see output |
--reads |
input read samples fastq/sam/bam file(s) |
--sample_id |
id to use for sample, goes in output files |
-
--max-threads: number of threads to use -
--seed: fixing the seed will produce the same outputs consistently
Under directory ./run/genotype:
- genotyped.vcf.gz
- genotyped.json: a JSON file counterpart to VCF which can describe nested variants
- personalised_reference.fasta
Under directory ./run/coverage, coverage files describing the result of mapping the reads to the prg.
They are described here.