fish_pedigree - Pedigree Chromosome Drawer

Fish-Pedigree

Fish-Pedigree is a set of Python3 scripts able to draw publication-ready vectorial chromosomes for pedigree and local ancestry inferance.

Description

Set of Python 3 scripts for creating a publication-ready vectorial chromosomes in Scalable Vector Graphics (SVG) format. The resulting file can either be submitted for publication and edited with any vectorial drawing software like Inkscape and Abobe Illustrator(R).

The necessary input files are a VCF file with SNP aligned to a reference genome, the reference genome (FASTA formatted) and the list of samples.

Installation

git clone https://github.com/pseudogene/fish_pedigree.git
cd fish_pedigree
python3 setup.py install

Usage

make_karyotype.py

The core script need to establish the length and structure of the genome, the script make_karyotype.py used the genome sequence (FASTA) used to aligned the SNP and create a BED file with the chromsosme structure.

Usage: make_karyotype.py --fasta FASTA [--circos]

Arguments:
  --fasta FASTA, -i FASTA
       Path to the genome file (FASTA format)
  --circos
       Format for CIRCOS rather than normal BED format

Example:
  make_karyotype.py --fasta tilapia_GCF_001858045.2.fasta > tilapia.bed

vcf2map.py

The script relaised on RFmix to generate the Ancestry inferences. RFmix requires a generic map. This pseudo-map can be generated from the alignement of the genome using this script: each chromosome length is rescaled from 1 to 100 and the markers/SNP position are located on this new ordinate system.

Usage: vcf2map.py --vcf VCF

Arguments
  --vcf VCF -i VCF
       Path to the VCF file aligned with the reference genome

Example:
  vcf2map.py --vcf tilapia_SNP.vcf > map.txt

map_chr.py

Following the run with RFmix, this script generate a meaning full output or visualisation.

Usage: map_chr.py --karyotype KARYOTYPE
                  [--msp MSP]
                  [--fb FB] [--t THRESHOLD]
                  [--chr CHRM] [--sample SAMPLE]
                  [--prefix PREFIX]
                  [--html] [--nojs]

Arguments:
  --msp MSP
        Path to RFmix MSP output
  --fb FB
        Path to RFmix FB output
  --t THRESHOLD
        Threshold for identification (use with FB file)
  --karyotype KARYOTYPE
       Path to the karyotype file (BED format)
  --chr CHRM
        Include only the specified chromosome
  --sample SAMPLE
        Include only the specified sample
  --prefix PREFIX
        Output prefix
  --html
        Output HTML format rather than BED format
  --nojs
        No dynamic HTML

Example:
  map_chr.py --msp tilapia.msp.tsv --karyotype tilapia.bed --html
  map_chr.py --fb tilapia.fb.tsv --t 0.75 --karyotype tilapia.bed --html --nojs

Pipeline examples

# Distribution test
map_chr.py --k examples/O_niloticus.bed --msp examples/O_niloticus.msp.tsv --html --prefix example

# Given snp.vcf (10 samples: 5 queries, 5 references), genome.fasta and sample_list.txt

make_karyotype.py --fasta genome.fasta > my_genome.bed
vcf2map.py --vcf snp.vcf > my_map.txt

# External software: BEAGLE
java -Xmx30688m -jar beagle.jar gt=snp.vcf out=phased

cut -f1-9,10-14 phased.vcf > query.vcf
cut -f1-9,15-19 phased.vcf > reference.vcf

# Externale software RFMIX
rfmix -f query.vcf -r reference.vcf -m sample_list.txt -g my_map.txt -o output --chromosome=chr1

map_chr.py --msp output.msp.tsv --karyotype my_genome.bed --html

How to cite fish_pedigree

Avallone, A., Bartie, K.L., Selly, S.-L.C., Taslima, K. Campos Mendoza, A., Bekaert, M. Local ancestry inference provides insight into Tilapia breeding programmes. Sci Rep, 10, 18613 (2020).

License

The content of this project itself is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License, and the source code presented is licensed under the GPLv3 license.