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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
sequence variant candidate that may cause Schizophrenia by a double hit
model (i.e., compound-heterozygosity or recessive model)
Run the commands step by step to see what will happen
1. Filter
by genetic feature and inheritance model (compound-heterozygosity or
recessive)
java -jar kggseq.jar --vcf-file
examples/rare.disease.hg19.vcf --ped-file
examples/rare.disease.ped.txt --out test1 --excel
--double-hit-gene-trio-filter
//when QC is imposed
java -jar kggseq.jar --vcf-file examples/rare.disease.hg19.vcf --ped-file
examples/rare.disease.ped.txt --out test1 --excel
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8
2. 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
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8 --db-gene refgene --gene-feature-in
0,1,2,3,4,5,6
3. 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
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8 --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6 --db-filter
1kg201204,dbsnp137,ESP6500AA,ESP6500EA --rare-allele-freq 0.01
4. 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
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8 --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter 1kg201204,dbsnp137,ESP6500AA,ESP6500EA --rare-allele-freq 0.02 --db-score
dbnsfp --mendel-causing-predict all --filter-nondisease-variant
5. 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
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8 --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter 1kg201204,dbsnp137,ESP6500AA,ESP6500EA --rare-allele-freq 0.02 --db-score
dbnsfp --mendel-causing-predict all --filter-nondisease-variant --genome-annot
--omim-annot
6. 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
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8 --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter 1kg201204,dbsnp137,ESP6500AA,ESP6500EA --rare-allele-freq 0.02 --db-score
dbnsfp --mendel-causing-predict all --filter-nondisease-variant --genome-annot
--candi-list LSM1,NRGN,SYNE1 --ppi-annot string --ppi-depth 1
7. 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
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8 --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter 1kg201204,dbsnp137,ESP6500AA,ESP6500EA --rare-allele-freq 0.02 --db-score
dbnsfp --mendel-causing-predict all --filter-nondisease-variant --genome-annot
--candi-list LSM1,NRGN,SYNE1 --ppi-annot string --ppi-depth 1 --pathway-annot
cura
8. 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
--double-hit-gene-trio-filter --seq-qual 50 --seq-mq 20 --seq-sb -10
--gty-qual 20 --gty-dp 8 --db-gene refgene --gene-feature-in 0,1,2,3,4,5,6
--db-filter 1kg201204,dbsnp137,ESP6500AA,ESP6500EA --rare-allele-freq 0.02 --db-score
dbnsfp --mendel-causing-predict all --filter-nondisease-variant --genome-annot
--candi-list LSM1,NRGN,SYNE1 --ppi-annot string --ppi-depth 1
--pathway-annot cura --pubmed-mining Schizophrenia
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