Indexing

Haplotype sampling mode

vg index

Usage: vg index [options] <graph1.vg> [graph2.vg ...]

Example grave command:

vg index --threads ${task.cpus} ${args} --dist-name ${distname} ${graph}

• ${args} set by --noNestedDistance, if true provides --no-nested-distance to vg index, & vg index will produce a limited distance index. This should only be set if users run into memory issues with complex graphs

vg gbwt

Usage: vg gbwt [options] [args]

vg haplotypes

Logic uses the ${types} variable, which is set based on the contents of the samplesheet (i.e., only ancient samples = ancient, only modern samples = modern, a mix = both). Based on this, only the required indexes will be built.

Usage: vg haplotypes [options] -H output.hapl graph.gbz

Example grave command:

vg haplotypes --threads ${task.cpus} --verbosity 2 --kmer-length ${params.aDNAkmerHaplSubSam} --window-length ${params.aDNAwindowHaplSubSam} --haplotype-output ${ahaplname} ${graph}

Filtered graph mode

vg index

vg minimizer