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config.yaml
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# analysis groups
samples:
ancestral_paths_v3:
reference: GRCh37
metadata: data/ancestral_paths_v3/ancestral_paths_v3.sampleInfo.tsv
genotypes: data/ancestral_paths_v3/ancestral_paths_v3.bcf
is_haploid: False
is_likelihood: False
populations:
all: {}
simulated_relate_painted:
reference: GRCh37
metadata: data/ancestral_paths_v3/simulated_relate_painted.sampleInfo.tsv
genotypes: data/ancestral_paths_v3/simulated_relate_painted.vcf.gz
is_haploid: False
is_likelihood: False
populations:
all: {}
ancestral_paths_new:
reference: GRCh37
metadata: data/Ancestral_paths_new/ancestral_paths_merged_filtered_age.sampleInfo.tsv
genotypes: data/Ancestral_paths_new/ancestral_paths_merged_filtered.bcf
is_haploid: False
is_likelihood: False
populations:
all: {}
chr3_true_paths:
reference: GRCh37
metadata: data/Ancestral_paths_new/simulation_metadata.tsv
genotypes: data/Ancestral_paths_new/chr3_simulated_true_painted.vcf.gz
is_haploid: False
is_likelihood: False
populations:
all: {}
chr3_inferred_paths:
reference: GRCh37
metadata: data/Ancestral_paths_new/simulation_metadata.tsv
genotypes: data/Ancestral_paths_new/chr3_simulated_inferred_painted.vcf.gz
is_haploid: False
is_likelihood: False
populations:
all: {}
imputed_unfiltered:
reference: GRCh37
metadata: data/Ancestral_paths_new/ancestral_paths_merged_filtered_age.sampleInfo.tsv
genotypes: data/imputed_unfiltered/ancestral_paths_new-all-chrALL-unfiltered-1000G.bcf
is_haploid: False
is_likelihood: False
populations:
all: {}
neo_likelihoods:
reference: GRCh37
metadata: data/Ancestral_paths_new/ancestral_paths_merged_filtered_age.sampleInfo.tsv
genotypes: data/neo.likelihoods/neo.likelihoods_merge.bcf
is_haploid: False
is_likelihood: True
populations:
all: {}
# list of chroms in GRCh37
chroms: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]
1000G:
pop_labels: data/1000G/1000G.poplabels
vcf_path: data/1000G/vcf/
anc_path: data/1000G/anc/
mask_path: data/1000G/mask/
map_path: data/1000G/map/
imputed:
vcf_path: /willerslev/users-shared/science-snm-willerslev-wl4sn3/step3_postprocessing/step5_release/15062020/
andres:
targets: data/andres/subset.gwascatalog.clinvar.merged.final.list.tsv
inv17_h1h2:
targets: data/andres/inv17_h1h2_snps.txt
mathieson:
targets: data/mathieson/41586_2015_BFnature16152_MOESM270_ESM.txt
# reference effective population size to scale c14 dates into diffusion units
nref: 10000
# average generation time in years
gen_time: 28
relate:
path: ../relate/
# human mutation rate
mu: 1.25e-8
# effective population size
Ne: 30000
# number of times branch lengths are sampled
num_samples: 100
clues:
path: ../clues/
harvester:
path: ../harvester/