Mercurial > repos > crs4 > kggseq_variant_selection
comparison examples/param.rare.disease.hg19.txt @ 4:a13b8ff61c6c draft
planemo upload
author | crs4 |
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date | Thu, 04 Aug 2016 04:40:06 -0400 |
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3:c758125c56d8 | 4:a13b8ff61c6c |
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1 #one argument per line | |
2 #I.Environmental setting | |
3 --buildver hg19 \ \ #line 1 | |
4 --nt 4 \ \ #line 2 | |
5 #--no-lib-check \ #line 3 | |
6 #--no-resource-check \ \ #line 4 | |
7 | |
8 #II. Specify the input files | |
9 --vcf-file examples/rare.disease.hg19.vcf \ #line 5 | |
10 --ped-file examples/rare.disease.ped.txt \ #line 6, or specify --indiv-pheno X:1,Y:1,Z:2 | |
11 | |
12 #III. Output setting | |
13 --out ./test1 \ #line 7 | |
14 --excel \ #line 8 | |
15 --o-vcf \ #line 10 | |
16 #--o-flanking-seq 50 \ #line 11, need large RAM memory | |
17 | |
18 #IV. QC | |
19 --gty-qual 10 \ #line 12 | |
20 --gty-dp 4 \ #line 13 | |
21 --gty-af-ref 0.05 \ #line 14 | |
22 --gty-af-het 0.25 \ #line 15 | |
23 --vcf-filter-in PASS,VQSRTrancheSNP90.00to93.00,VQSRTrancheSNP93.00to95.00,VQSRTrancheSNP95.00to97.00,VQSRTrancheSNP97.00to99.00 \ #line 16 | |
24 --seq-qual 50 \ #line 17 | |
25 --seq-mq 20 \ #line 18 | |
26 --seq-fs 60 \ #line 19 | |
27 --min-obsa 1 \ #line 20 | |
28 #V. Filtering | |
29 | |
30 --genotype-filter 1,2,6 \ #line 22 for recessive mode | |
31 #--ibs-case-filter 1000 \ #line 23, or specify 'ibdregions.txt' file | |
32 --regions-out chrX,chrY \ #line 22 | |
33 --db-filter 1kg201204,dbsnp141,ESP6500AA,ESP6500EA \ #line 26 | |
34 --rare-allele-freq 0.006 \ #line 27 | |
35 --db-filter-hard dbsnp138nf \ #line 27 | |
36 --db-gene refgene,gencode,knowngene \ #line 24 | |
37 --gene-feature-in 0,1,2,3,4,5,6 \ #line 25 | |
38 --superdup-filter \ | |
39 --gene-var-filter 4 | |
40 | |
41 #VI. Annotation | |
42 --scsnv-annot \#line 31 | |
43 --dgv-cnv-annot --candi-list ECEL1,MYBPC1,TNNI2,TNNT3,TPM2 \#line 31 | |
44 --geneset-annot cura \ #line 33 | |
45 --ppi-annot string \ #line 34 | |
46 --ppi-depth 1 \ #line 35 | |
47 --phenotype-term Arthrogryposis,Arthrogryposis+multiplex+congenita \ #line 35 | |
48 --pubmed-mining | |
49 | |
50 #VII. Prediction at variants | |
51 --db-score dbnsfp \ #line 28 | |
52 --mendel-causing-predict all | |
53 --filter-nondisease-variant \ #line 29 | |
54 | |
55 #VIII. Prediction at genes | |
56 --patho-gene-predict | |
57 #--phenolyzer-prediction |