Annotate VCF with snpeff and bcsq
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ANNOTATION-NF
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nextflow main.nf --debug
nextflow main.nf --vcf=hard-filtered.vcf --species=c_elegans --divergent_regions=divergent_regions_strain.bed
parameters description Set/Default
========== =========== ========================
--debug Set to 'true' to test ${params.debug}
--species Species: 'c_elegans', 'c_tropicalis' or 'c_briggsae' ${params.species}
--vcf hard filtered vcf to calculate variant density ${params.vcf}
--divergent_regions (Optional) Divergent region bed file ${params.divergent_regions}
--reference Reference used based on species and project ${params.reference}
--output (Optional) output folder name ${params.output}
username ${"whoami".execute().in.text}
HELP: http://andersenlab.org/dry-guide/pipeline-annotation-nf
- The latest update requires Nextflow version 20.0+. On QUEST, you can access this version by loading the
nf20_envconda environment prior to running the pipeline command:
module load python/anaconda3.6
source activate /projects/b1059/software/conda_envs/nf20_env
Alternatively you can update Nextflow by running:
nextflow self-update
This command uses a test dataset
nextflow run andersenlab/annotation-nf --debug
You should run this in a screen session.
nextflow run andersenlab/annotation-nf --vcf <path_to_vcf> --species <species> --divergent_regions <path_to_file>
You should use --debug true for testing/debugging purposes. This will run the debug test set (located in the test_data folder).
For example:
nextflow run andersenlab/annotation-nf --debug
Path to the hard-filter, isotype VCF (output from post-gatk-nf)
Choose from c_elegans, c_briggsae, or c_tropicalis. Species will specifiy a default reference genome. You can select a different one if you prefer (see below)
This is the divergent_regions_strain.bed file output from the post-gatk-nf pipeline. This file is used to add a column to the flat file if the variant is within a divergent region. Currently, C. elegans is the only species with divergent regions, if running for another species, do not provide a divergent_regions file and the pipeline will ignore it.
By default, the reference genome is set by the species parameter. If you don't want to use the default, you could change the project and/or ws_build. As long as the genome is in the proper location on quest (for more, see the genomes-nf pipeline), this will work. Alternatively, you could provide the path to a reference of your choice.
Defaults:
- C. elegans -
/projects/b1059/data/c_elegans/genomes/PRJNA13758/WS276/c_elegans.PRJNA13758.WS276.genome.fa.gz - C. briggsae -
/projects/b1059/data/c_briggsae/genomes/QX1410_nanopore/Feb2020/c_briggsae.QX1410_nanopore.Feb2020.genome.fa.gz - C. tropicalis -
/projects/b1059/data/c_tropicalis/genomes/NIC58_nanopore/June2021/c_tropicalis.NIC58_nanopore.June2021.genome.fa.gz
This parameter is necessary for correct annotation using BCSQ for variants with many different annotations (like found in divergent regions). In 20210121 we found that the default value of 224 was sufficient, but as more strains are added this number might need to increase. If there is an issue, you should see a warning error from BCFtools and they should suggest what to change this parameter to.
├── strain_vcf
│ ├── {strain}.{date}.vcf.gz
│ └── {strain}.{date}.vcf.gz.tbi
└── variation
├── WI.{date}.hard-filter.isotype.snpeff.vcf.gz
├── WI.{date}.hard-filter.isotype.snpeff.vcf.gz.tbi
├── snpeff.stats.csv
├── WI.{date}.hard-filter.isotype.bcsq.vcf.gz
├── WI.{date}.hard-filter.isotype.bcsq.vcf.gz.tbi
├── WI.{date}.hard-filter.isotype.bcsq.vcf.gz.stats.txt
└── WI.{date}.strain-annotation.bcsq.tsv