Vg deconstruct

Call variants in the graph

vg deconstruct

Outputs VCF of snarls (bubbles) in the graph, one line per site (bubble). Coordinates and reference alleles are based off the reference paths, while alt alleles come from all other paths in the graph. Read more here.

Usage: vg deconstruct [options] [-p|-P] <PATH> <GRAPH>

Example grave command:

vg deconstruct -t ${task.cpus} ${graph} --snarls ${snarls} --all-snarls --gbz-translation | bgzip --threads ${task.cpus} > ${basename}.raw.vcf.gz

tabix

Indexes VCF files for fast data retrieval.

Usage: tabix [OPTIONS] [FILE] [REGION [...]]

Example grave command:

tabix -p vcf ${basename}.raw.vcf.gz

vcfbub

Processes the VCF, discarding nested variants over (--maxNestLevel), unless found within a popped feature. Popped features are those with reference allele length over (--maxRefLength).

Usage: vcfbub [FLAGS] [OPTIONS] --input <FILE>

Example grave command:

vcfbub --input ${basename}.raw.vcf.gz --max-level ${params.maxNestLevel} --max-ref-length ${params.maxRefLength}

bcftools norm

Left-align and normalize indels.

Usage: bcftools norm [options] <in.vcf.gz>

Example grave command:

bcftools norm -f ${reference_fasta}

bcftools sort

Sorts variants to genome order.

Usage: bcftools sort [OPTIONS] <FILE.vcf>

Example grave command:

bcftools sort