-
Notifications
You must be signed in to change notification settings - Fork 0
Variant callers
Prints coverage statistics from the input BAM file and converts to regions with even sequencing coverage for parallelisation of freebayes.
Usage:
bamtools [--help] COMMAND [ARGS] | /opt/conda/bin/coverage_to_regions.py fasta_index num_regions >regions.bed
Example grave command:
bamtools coverage -in ${bams} | coverage_to_regions.py ${fasta_index} 500 > ${reference_fasta}.regions
Runs freebayes in parallel over regions listed in the regions file, using ncpus processors. Will merge and sort output, producing a uniform VCF stream on stdout.
Usage:
freebayes-parallel [regions file] [ncpus] [freebayes arguments]
Example grave command:
freebayes-parallel ${reference_fasta}.regions ${task.cpus} --genotype-qualities --fasta-reference ${reference_fasta} --min-alternate-count ${params.minimumAlleleSupport} --min-alternate-fraction ${params.minFraction} --ploidy ${params.samplePloidy} --max-complex-gap ${params.maxComplexGap} ${bams}
Left-align and normalize indels.
Usage:
bcftools norm [options] <in.vcf.gz>
Example grave command:
bcftools norm -f ${reference_fasta} ${meta.id}.raw.vcf.gz
Sorts variants to genome order.
Usage:
bcftools sort [OPTIONS] <FILE.vcf>
Example grave command:
bcftools sort
Run the pangenome aware version of DeepVariant. Note this is currently only recommended for human samples due to the training of the underlying model.
Usage:
run_pangenome_aware_deepvariant.py [options]
Example grave command:
/opt/deepvariant/bin/run_pangenome_aware_deepvariant --num_shards ${task.cpus} --sample_name_reads ${meta.id} --ref ${reference_fasta} --pangenome ${graph} --reads ${bams} --output_vcf ${meta.id}.raw.vcf.gz --vcf_stats_report --model_type ${params.deepVariantModelType}
Left-align and normalize indels.
Usage:
bcftools norm [options] <in.vcf.gz>
Example grave command:
bcftools norm -f ${reference_fasta} ${deepvariant_vcf}
Sorts variants to genome order.
Usage:
bcftools sort [OPTIONS] <FILE.vcf>
Example grave command:
bcftools sort