forked from titansmc/pipeline
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Snake.config.json
50 lines (40 loc) · 1.73 KB
/
Snake.config.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
{
"chromosomes" : ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX"],
"reference" : "/MMCI/TM/scratch/ref/GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
"mosaicatcher" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/git/build/mosaic",
"plot_script" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/git/R/qc.R",
"samtools" : "samtools",
"bcftools" : "bcftools",
"snv_sites_to_genotype": "snv_sites_to_genotype/ALL.chr1-22plusX_GRCh38_sites.20170504.renamedCHR.vcf.gz",
"snv_calls" : {},
"variable_bins" : {
"50000" : "utils/variable_bins.GRCh38.50kb.bed",
"100000" : "utils/variable_bins.GRCh38.100kb.bed"
},
"R_reference" : "BSgenome.Hsapiens.UCSC.hg38",
"bp_density" : {
"few" : 0.2,
"medium" : 0.4,
"many" : 0.6
},
"paired_end" : true,
"simulation_min_vaf" : 0.01,
"simulation_max_vaf" : 1.0,
"simulation_neg_binom_p" : {
"50000" : 0.4,
"100000" : 0.3,
"500000" : 0.1
},
"simulation_min_reads_per_library" : 500000,
"simulation_max_reads_per_library" : 1000000,
"simulation_window_sizes" : [50000, 100000],
"simulation_cell_count" : 100,
"simulation_alpha" : 0.02,
"genome_size" : 3e9,
"ground_truth_clonal" : {
"RPE-BM510" : "/MMCI/TM/scratch/strandseq/input-data/ground_truth/RPE-BM510_manual/clonal-events.tsv"
},
"ground_truth_single_cell" : {
"RPE-BM510" : "/MMCI/TM/scratch/strandseq/input-data/ground_truth/RPE-BM510_manual/single-cell-events.tsv"
}
}