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config.yaml
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config.yaml
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samplemetadata: "metadata/samples.csv"
classifier_training_data: "refdata/human/classifier_training_data.h5"
reference_gc: refdata/human/reference_gc_grch37.csv
refdir: refdata/
thousand_genomes_snps: refdata/human/thousand_genomes_snps.tsv
ref_genome: refdata/human/GRCh37-lite.fa
mappability:
local_path: refdata/human/wgEncodeCrgMapabilityAlign50mer.bigWig
url: http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/release3/wgEncodeCrgMapabilityAlign50mer.bigWig
signals:
mincells: 5
qualfilter: 0.0
# refdata/human/GRCh37-lite.gc.ws_500000.wig
#refdata/human/GRCh37-lite.map.ws_125_to_500000.wig
hmmcopy:
bin_size: 200000
gc_wig_file: hmmcopy_wigfiles/wigfiles/grch37/GRCh37-lite.gc.ws_200000.wig
map_wig_file: hmmcopy_wigfiles/wigfiles/grch37/GRCh37-lite.map.ws_200000.wig
ref_genome: refdata/human/GRCh37-lite.fa
chromosomes:
- '1'
- '2'
- '3'
- '4'
- '5'
- '6'
- '7'
- '8'
- '9'
- '10'
- '11'
- '12'
- '13'
- '14'
- '15'
- '16'
- '17'
- '18'
- '19'
- '20'
- '21'
- '22'
- X
- Y
docker:
hmmcopy: hmmcopy:v0.0.6
single_cell_pipeline: single_cell_pipeline:v0.6.41
e: 0.999999
eta: 50000
exclude_list: refdata/human/repeats.satellite.regions
g: 3
good_cells:
- - median_hmmcopy_reads_per_bin
- ge
- 50
- - is_contaminated
- in
- - 'False'
- 'false'
- false
igv_segs_quality_threshold: 0.75
kappa: "100,100,700,100,25,25,25,25,25,25,25,25"
lambda: 20
m: "0,1,2,3,4,5,6,7,8,9,10,11"
map_cutoff: 0.9
memory:
med: 6
min_mqual: 20
mu: "0,1,2,3,4,5,6,7,8,9,10,11"
multipliers: "1,2,3,4,5,6"
nu: 2.1
num_states: 12
s: 1
smoothing_function: modal
strength: 1000
infer_haps:
chromosomes:
- '1'
- '2'
- '3'
- '4'
- '5'
- '6'
- '7'
- '8'
- '9'
- '10'
- '11'
- '12'
- '13'
- '14'
- '15'
- '16'
- '17'
- '18'
- '19'
- '20'
- '21'
- '22'
- X
- Y
extract_seqdata:
genome_fai_template: refdata/human/GRCh37-lite.fa.fai
genome_fasta_template: refdata/human/GRCh37-lite.fa
max_cores: null
memory:
high: 16
low: 4
med: 6
ref_data_dir: refdata/human/