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