perEditor

A tool to create personalized genome sequences

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Tutorial

To help you understand how perEditor and perEditor_ra work you can try the following examples.

perEditor

First, download these samples files.

chr1.fa: reference sequence in fasta format.

variations.vcf: SNP/indels annotation VCF file. This file contains information about 629 individuals. For each individual the VCF file specifies if the variations is on the maternal or paternal chromosome.

Go to the folder where you have  downloaded these files and type:

perEditor chr1.fa variations.vcf mother 1 chr1_customized.fa

This will tell to perEditor that chr1.fa is the reference sequence that is going to be customized using the information contained in variations.vcf. As variations.vcf contain information about several individuals (629) we are specifying that we want a customized reference relative to the maternal allele (mother) of the first individual (1). The customized reference sequence will be stored as chr1_customized.fa.

perEditor_ra

Download a set of sample input files from here. These sample files include four chromosomes (fasta files), a rearrangement file (VCF 4.1 format), and two BED files with information about the length of each chromosome and the location of its centromeres, respectively. The rearrangement file specifies the following chromosomal modifications:

Once you have downloaded these files in a folder, go to that folder and type:

perEditor_ra rearrangements_t.vcf chr_length_t.bed centromeres_t.bed 1 father

This will tell perEditor_ra that you are interested in the parternal (father) allele of the first (1) individual. After do so, perEditor_ra will create four new chromosomes, namely chr1_new.fa, chr2_new.fa, chr3_new.fa, and chr4_new.fa that have been modified to show the rearrangement contained in the rearrangements_t.vcf file.