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Input data:
1. A
Variant Call Format (VCF) file (a simulated data set)
examples/rare.disease.hg19.vcf
2. A
linkage pedigree file:
examples/rare.disease.ped.txt
Purpose: Identify
de novo sequence mutation that may cause Crohn's disease
Run the commands step by step to see what will happen
1. Direct
filter
by de
novo events and QC
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
7
2. Filter
out
the de novo mutations where both affected and unaffected subjects have the
same heterozygous genotypes and the same ALTERNATIVE homozygous genotypes
java -jar kggseq.jar
--vcf-file examples/rare.disease.hg19.vcf --ped-file
examples/rare.disease.ped.txt --out test1 --excel --seq-qual 50
--seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp 8 --gty-sec-pl 20
--gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo
3. Annotate
sequence variants by RefGenes:
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
4. Filter
sequence variants by Common variants
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6 --db-filter
dbsnp138,ESP5400 --rare-allele-freq 0.05
5. Prioritize
sequence variants by disease-causing prediction
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter dbsnp138,ESP5400 --rare-allele-freq 0.05 --db-score
dbnsfp --mendel-causing-predict all --filter-nondisease-variant
6. Prioritize
sequence variants by other genomic and OMIM annotation
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter dbsnp138,ESP5400 --rare-allele-freq 0.05 --db-score dbnsfp
--mendel-causing-predict all --filter-nondisease-variant --genome-annot
--omim-annot
7. Prioritize
sequence variants by candidate genes with protein interaction
information
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter dbsnp138,ESP5400 --rare-allele-freq 0.05 --db-score dbnsfp
--mendel-causing-predict all --filter-nondisease-variant --genome-annot
--omim-annot --candi-list ATG16L1,IL23R,IRGM --ppi-annot string
--ppi-depth 1
8. Prioritize
sequence variants by candidate genes with pathway information
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter dbsnp138,ESP5400 --rare-allele-freq 0.05 --db-score dbnsfp
--mendel-causing-predict all --filter-nondisease-variant --genome-annot
--omim-annot --candi-list ATG16L1,IL23R,IRGM --ppi-annot string --ppi-depth
1 --pathway-annot cura
9. Prioritize
sequence variants by PubMed
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file examples/rare.disease.ped.txt --out
test1 --excel --seq-qual 50 --seq-mq 20 --seq-sb -10 --gty-qual 20 --gty-dp
8 --gty-sec-pl 20 --gty-af-ref 0.05 --gty-af-het 0.25 --gty-af-alt 0.75 --genotype-filter
4,7 --ignore-homo --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter dbsnp138,ESP5400 --rare-allele-freq 0.05 --db-score dbnsfp
--mendel-causing-predict all --filter-nondisease-variant --genome-annot
--omim-annot --candi-list ATG16L1,IL23R,IRGM --ppi-annot string --ppi-depth
1 --pathway-annot cura --pubmed-mining Crohn\'s+disease,inflammatory+bowel+disease
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