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config.yml
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#=======================================================#
# gust config file #
# most of this file is comments, which you can delete #
#=======================================================#
fragment_size: 150
# size of the sliding window genome fragments
# values of 50-300+ should be ok (use your judgement)
# note: bwa isn't good at mapping really long sequences
reference_genome: "genome.fasta"
# name of reference genome in the genomes/ dir
outgroup: "outgroupgenome.fasta"
# name of the outgroup genome in the genomes/ dir
bwa_parameters: "-a -k 19"
# -a outputs all alignments
# -k 19 is a kmer size of 19
freebayes_parameters: "-C 1 --min-coverage 5 --standard-filter --ploidy 1"
# -C 2 means at least 2 samples need to have alt alleles for a site to be kept
# --min-coverage 5 means at least 5 aligments to score a site
# --standard-filter is to add more stringency
# --ploidy 1 because these are typically haploid assemblies
window_size: 20000
# window size in base pairs for LD pruning snp data
# bigger window = fewer snps
sites_per_window: 10
# number of sites to keep per window
mafft_parameters: "--auto --maxiterate 1000 --nuc"
# --auto chooses the appropriate model for the data size
# --maxiterate is the max number of iterations for tree building
# --nuc is to specify the input is nucleotides
raxml_model: "GTR+G"
# the phylogenetic model you would like to use, see for options:
# https://isu-molphyl.github.io/EEOB563/computer_labs/lab4/models.html
raxml_parameters: '--bs-trees 100 --tree pars\{25\},rand\{25\} -brlen scaled'
# --bs-trees 100 is 100 bootstrapped trees
# --tree pars{25},rand{25} is to use 25 parsimonious trees and 25 random trees
# the curly braces need to be escaped with \ for snakemake and note the single quotes
# -brlen scaled is the model for branch linkage