Emblask/params.yaml at main · DecodeGenetics/Emblask · GitHub

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
### PIPELINE INPUT ###

proband_lr_bam_in: ""
proband_lr_fq_in: ""

proband_sr_bam_in: ""
proband_sr_fq_in: "" # IMPORTANT: This MUST be an interleaved FASTQ file!

father_sr_bam_in: ""
father_sr_fq_in: ""

mother_sr_bam_in: ""
mother_sr_fq_in: ""

out_dir: ""

# Size of the genome to assemble in bp for long reads subsampling, e.g. 3100000000 for human
# Only use if input long read coverage is >50x
# Default value is -1 (no subsampling)
genome_size: -1

# Maximum base quality of the input long reads
# This pipeline is designed for ONT R9.4 long reads for which the maximum base quality SHOULD be 40
# However, ONT R10 long read data seems to use a maximum base quality of 90
max_lr_bq: 40

### PIPELINE CONFIG ###

# This pipeline uses default models trained on ONT R9.4 long reads corrected with Illumina for Pepper-Margin-DeepVariant r0.7
# These models are assumed to be available by default in pmdv/r07/models/ratatosk_r9_guppy5_sup
# However, it is possible to supply here your own models which will override the default ones
# Make sure to leave empty in order to use the default models
pmdv_r07_model_r9_guppy5_sup_snp: ""
pmdv_r07_model_r9_guppy5_sup_hp: ""
pmdv_r07_model_r9_guppy5_sup_dv: ""