-
Notifications
You must be signed in to change notification settings - Fork 0
/
config.yaml
59 lines (47 loc) · 1.51 KB
/
config.yaml
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
51
52
53
54
55
56
57
58
59
fastq_dir: "test/fastq_dir"
output_dir: "test/output"
ref: "test/ref/CC1.8_v2_pseudomolecule_cat.fa"
## quality control before processing
fastqc:
params: ""
threads: 2
## pre-processing if neccessary
# fastp
## variant calling from fastq
bwa_mem:
params: "-R '@RG\tID:RC3\tSM:RC3\tPL:Illumina'"
threads: 2
mem: ""
picard_SortSam:
params: "-SORT_ORDER coordinate -VALIDATION_STRINGENCY SILENT" # index reference
mem: ""
samtools_view:
params: "-h -b -f 0x02" # convert sam to bam and filter mapping
threads: 48
mem: ""
MarkDuplicates:
params: "--remove-sequencing-duplicates false --read-validation-stringency SILENT"
threads: 2
mem: ""
HaplotypeCaller:
params: "--read-filter GoodCigarReadFilter --annotate-with-num-discovered-alleles true --max-alternate-alleles 10"
threads: 2
mem: "50G"
CombineGVCFs:
params: ""
mem: ""
GenotypeGVCFs:
params: ""
mem: ""
## stats before and/or after variant filtration
## variant filtration
gatk_VariantFiltration:
params: "--cluster-size 4 --cluster-window-size 10 --filter-name 'LOW-QUAL' --filter-expression 'QUAL<200' --filter-name 'LOW-MQ' --filter-expression 'MQ0>=4 && ((MQ0/(1.0 * DP)) > 0.1 )' "
suffix: "_VariantFiltration"
gatk_SelectVariants:
params: "--restrict-alleles-to BIALLELIC --select-type-to-include SNP"
suffix: "_SelectVariants"
vcftools:
params: "--min-meanDP 10 --max-meanDP 100 --max-missing 0.85" # singleton, doubleton
suffix: "_vcftools"
filtration_mem: ""