Quickstart

GRAFIMO usage options

To check out all usage instructions available for GRAFIMO type

grafimo --help  # or grafimo -h

GRAFIMO VG scan

Scannig a genome variation graph (built constructing graph for each chromosome) for the occurrences of a DNA motif in a set of genomic regions defined in a BED file. Note that the motif(s) can be given in MEME or JASPAR format.

grafimo -d /path/to/directory/stroring/my/graphs/ -b /path/to/my/bedfile -m path/to/mt/motif

Scanning a whole genome graph for the occurrences of a DNA motif in a set of genomic regions defined in a BED file. Note that the motif(s) can be given in MEME or JASPAR format.

grafimo -g /path/to/my/whole/genome/vg -b /path/to/my/bedfile -m /path/to/my/motif

GRAFIMO VG build

Building the genome variation graph with GRAFIMO (GRAFIMO will build a graph for each single chromosome). Note that the names of chromosomes must be identical on both the reference genome and the VCF file containing the genomic variants; for example if in the VCF the chromosome 1 is named as 1, the reference genome FASTA file must contain >1 instead of >chr1 in chromosome 1 sequence header.

grafimo buildvg -l /path/to/reference/genome -v /path/to/vcf/file