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config.yaml
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mode: all
flow: ibis
ibis_seg_len: 7.0
ibis_min_snp: 500
zero_seg_count: 0.5
zero_seg_len: 5.0
alpha: 0.01
num_batches: 1
samples_file: samples.tsv
vcf_file: vcf/merged.vcf.gz
use_simulated_ibd: False
use_ibis: False
ref_dir: /media/ref
azure_public_key: "?sv=2022-11-02&ss=f&srt=o&sp=r&se=2026-01-24T00:45:07Z&st=2024-01-16T17:45:07Z&spr=https&sig=1M3m%2BnsAujxopJDwgEB%2FIGRMBWLxFS0WvXr0SqAbBTc%3D"
1000g_public_key: "?sv=2019-10-10&si=prod&sr=c&sig=9nzcxaQn0NprMPlSh4RhFQHcXedLQIcFgbERiooHEqM%3D"
reference:
GRCh37_fasta:
file: human_g1k_v37.fasta
url: https://dataset1000genomes.blob.core.windows.net/dataset/technical/reference/human_g1k_v37.fasta.gz
filesize: 892331003
md5: 45f81df94f0408d082363e34a081ed81
GRCh37_fasta_fai:
file: human_g1k_v37.fasta.fai
url: https://dataset1000genomes.blob.core.windows.net/dataset/technical/reference/human_g1k_v37.fasta.fai
filesize: 2746
md5: 772484cc07983aba1355c7fb50f176d4
GENETIC_MAP:
file: tables/genetic_map_hg19_withX.txt.gz
url: https://storage.googleapis.com/broad-alkesgroup-public/Eagle/downloads/tables/genetic_map_hg19_withX.txt.gz
filesize: 52604097
md5: 930ba8e1435d54f68fb7a723fd3f0fa4
mirror:
- https://data.broadinstitute.org/alkesgroup/Eagle/downloads/tables/genetic_map_hg19_withX.txt.gz
genetic_map_GRCh37:
file: genetic_map_GRCh37/genetic_map_GRCh37_chr{chrom}.txt
url: https://ftp-trace.ncbi.nih.gov/hapmap/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz
filesize: 37730100
md5: 1bc10a34d985e68e1f38ceb137b87929
phased_ref:
file: 1000genome/phased/chr{chrom}.phased.vcf.gz
vcfRef:
file: 1000genome/bcf/1000genome_chr{chrom}.bcf
url: https://dataset1000genomes.blob.core.windows.net/dataset/release/20130502/supporting/bcf_files/ALL.chr$chrom.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf
md5: [
'01aa2085294f4ea536ffcbe10d358799', # 1
'a80e9a4c5803780a31af7f2792a8b477', # 2
'5932947af13c1b36ab22bc8309f78edd', # 3
'ce56c2ff82096bf9a3cddf1fe58f3108', # 4
'9d59acd79f332aeccba0948521b225d0', # 5
'c7dd6a87dcbb29101a94732f5cf39c33', # 6
'87357436adcfcdfff11c7695e148b144', # 7
'b5ddd515912dc249d0e0ecb187369c0e', # 8
'fcc19b4c1694d93c69c42e1df0a044af', # 9
'e829cbaf375a03ab093b7757621fb664', # 10
'd34a8830e29a4b3acdb55cb61ddfa5b5', # 11
'5edb5af56dca5e879e7269445a5f50f6', # 12
'6e0ba8beb30e7b33d864a51f067c7909', # 13
'f5f251496e83d2cc706f2958dd0f8be2', # 14
'b87ad44ed1133eadab70f33fc1f317ae', # 15
'11dead39b8afc14adbc27bd7ca8a03c7', # 16
'25dd4a8365f426408acef6bf524e0783', # 17
'15b1f7aa48f655d524db31ae109e9233', # 18
'a5513ae3019d1a42ef3f1dfbf4199005', # 19
'60373f96173074bba27540ea099c4c7b', # 20
'c63dd9cf0018883b4492c70983c9c2cd', # 21
'5fbd47ed6b9edc15690e5fba07da2796', # 22
]
expand_rule:
key: $chrom
values: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]
filesize: [1004154825, 1084633520, 914542487, 922149598, 817845111, 826636182, 750819249, 711662593, 556593410, 639802490, 633698676, 613099190, 460817078, 418899669, 378463530, 408443782, 358580396, 360946073, 295923706, 282457469, 180550985, 177178725]
refHaps:
file: Minimac/{chrom}.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz
lift_chain:
file: hg38ToHg19.over.chain.gz
url: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/liftOver/hg38ToHg19.over.chain.gz
filesize: 1246411
md5: ff3031d93792f4cbb86af44055efd903
cmmap:
file: genetic_map_b37/genetic_map_chr{chrom}_combined_b37.txt
url: https://www.dropbox.com/s/slchsd0uyd4hii8/genetic_map_b37.zip
filesize: 50554370
md5: 8d7d0bf2bfd13a39cad0e8d5012666a2
SITE_1000GENOME:
file: 1000genome/allele_info/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.only_rs.biallelic.tab
url: https://dataset1000genomes.blob.core.windows.net/dataset/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5c.20130502.sites.vcf.gz
filesize: 1458224240
md5: d9c22df30ea810d5c7d98391e482d1a3
affymetrix_chip:
file: 1000genome/affymetrix_chip/all.vcf.gz
url: https://dataset1000genomes.blob.core.windows.net/dataset/release/20130502/supporting/hd_genotype_chip/ALL.wgs.nhgri_coriell_affy_6.20140825.genotypes_has_ped.vcf.gz
filesize: 782884333
md5: 019d00c28c1ff60906f72c11f7997c4c
pedsim_map:
file: refined_mf.simmap
url: https://github.com/cbherer/Bherer_etal_SexualDimorphismRecombination/raw/master/Refined_genetic_map_b37.tar.gz
filesize: 41278300
md5: 39e6e8620d616362875f2538eae2f279
bundle:
file: ref.tar.gz
url: https://bioinformatics.file.core.windows.net/bundles/ref_v2.tar.gz
filesize: 19411359855
md5: 300fa3e768b677958a2b8e270115c6d9
bundle_min:
file: ref_min.tar.gz
url: https://bioinformatics.file.core.windows.net/bundles/ref_min.tar.gz
filesize: 3074816502
md5: 15002b7eb18e3b991c16ef1131c4cc42
picard:
file: picard.jar
url: https://github.com/broadinstitute/picard/releases/download/2.26.2/picard.jar