Mercurial > repos > crs4 > kggseq_variant_selection
view examples/param.rare.disease.hg19.txt @ 5:ed0dbb61f0e1 draft
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author | crs4 |
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date | Thu, 04 Aug 2016 05:53:40 -0400 |
parents | a13b8ff61c6c |
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#one argument per line #I.Environmental setting --buildver hg19 \ \ #line 1 --nt 4 \ \ #line 2 #--no-lib-check \ #line 3 #--no-resource-check \ \ #line 4 #II. Specify the input files --vcf-file examples/rare.disease.hg19.vcf \ #line 5 --ped-file examples/rare.disease.ped.txt \ #line 6, or specify --indiv-pheno X:1,Y:1,Z:2 #III. Output setting --out ./test1 \ #line 7 --excel \ #line 8 --o-vcf \ #line 10 #--o-flanking-seq 50 \ #line 11, need large RAM memory #IV. QC --gty-qual 10 \ #line 12 --gty-dp 4 \ #line 13 --gty-af-ref 0.05 \ #line 14 --gty-af-het 0.25 \ #line 15 --vcf-filter-in PASS,VQSRTrancheSNP90.00to93.00,VQSRTrancheSNP93.00to95.00,VQSRTrancheSNP95.00to97.00,VQSRTrancheSNP97.00to99.00 \ #line 16 --seq-qual 50 \ #line 17 --seq-mq 20 \ #line 18 --seq-fs 60 \ #line 19 --min-obsa 1 \ #line 20 #V. Filtering --genotype-filter 1,2,6 \ #line 22 for recessive mode #--ibs-case-filter 1000 \ #line 23, or specify 'ibdregions.txt' file --regions-out chrX,chrY \ #line 22 --db-filter 1kg201204,dbsnp141,ESP6500AA,ESP6500EA \ #line 26 --rare-allele-freq 0.006 \ #line 27 --db-filter-hard dbsnp138nf \ #line 27 --db-gene refgene,gencode,knowngene \ #line 24 --gene-feature-in 0,1,2,3,4,5,6 \ #line 25 --superdup-filter \ --gene-var-filter 4 #VI. Annotation --scsnv-annot \#line 31 --dgv-cnv-annot --candi-list ECEL1,MYBPC1,TNNI2,TNNT3,TPM2 \#line 31 --geneset-annot cura \ #line 33 --ppi-annot string \ #line 34 --ppi-depth 1 \ #line 35 --phenotype-term Arthrogryposis,Arthrogryposis+multiplex+congenita \ #line 35 --pubmed-mining #VII. Prediction at variants --db-score dbnsfp \ #line 28 --mendel-causing-predict all --filter-nondisease-variant \ #line 29 #VIII. Prediction at genes --patho-gene-predict #--phenolyzer-prediction