Reference:
https://pmglab.top/kggseq/doc10/UserManual.html
Input data:
1.
A toy VCF file,
examples/simu100.coding.vcf.gz
2. A
conventional pedigree file, examples/simu100.ped
3. A
text file containing rare mutations sets, examples/ref.mutationrate.txt
4. A
text file containing additional covariates of genes, examples/genecov.txt
Purpose: Identify
susceptibility genes with rare coding variants for schizophrenia
Run the commands step by step to see what will happen
1.
Burden test at genes with rare coding
mutations by RUNNER
java -Xmx6g -jar kggseq.jar
--nt 4 --no-web --vcf-file examples/simu100.coding.vcf.gz --ped-file
examples/simu100.ped --out test1 --excel --db-filter
gadexome.eas,gadgenome.eas,1kgeas201305 --rare-allele-freq 0.01
--min-case-control-freq-ratio 3 --qqplot --gene-freq-score eas --db-score
dbnsfp --disease-causing-predict best --RUNNER-gene-coding
2.
Burden test by RUNNER with a reference
java -Xmx6g -jar
kggseq.jar --nt 4 --no-web --vcf-file examples/simu100.coding.vcf.gz
--ped-file examples/simu100.ped --out test1 --excel --db-filter
gadexome.eas,gadgenome.eas,1kgeas201305 --rare-allele-freq 0.01
--min-case-control-freq-ratio 3 --qqplot --gene-freq-score eas --db-score
dbnsfp --disease-causing-predict best --runner-gene-coding --ref-mut-sample
examples/ref.mutationrate.txt
3.
Burden test by RUNNER with additional
covariates of genes
java -Xmx6g -jar
kggseq.jar --nt 4 --no-web --vcf-file examples/simu100.coding.vcf.gz
--ped-file examples/simu100.ped --out test1 --excel --db-filter
gadexome.eas,gadgenome.eas,1kgeas201305 --rare-allele-freq 0.01
--min-case-control-freq-ratio 3 --qqplot --gene-freq-score eas --db-score
dbnsfp --disease-causing-predict best --runner-gene-coding --gene-cov-file
examples/genecov.txt
4.
Burden test by RUNNER using local
control samples
java -Xmx6g -jar
kggseq.jar --nt 4 --no-web --vcf-file examples/simu100.coding.vcf.gz
--ped-file examples/simu100.ped --out test1 --excel --db-filter
gadexome.eas,gadgenome.eas,1kgeas201305 --rare-allele-freq 0.01
--min-case-control-freq-ratio 3 --qqplot --gene-freq-score CONTROL
--db-score dbnsfp --disease-causing-predict best --runner-gene-coding
5.
Burden test by RUNNER at other types
of coding variants
java -Xmx6g -jar
kggseq.jar --nt 4 --no-web --vcf-file examples/simu100.coding.vcf.gz
--ped-file examples/simu100.ped --out test1 --excel --db-filter
gadexome.eas,gadgenome.eas,1kgeas201305 --rare-allele-freq 0.01 --min-case-control-freq-ratio
3 --qqplot --gene-freq-score eas --response-gene-feature
2,3,4,5,6 --db-score dbnsfp --disease-causing-predict best --runner-gene-coding
6.
Burden test at genes with rare coding
mutations by unweighted RUNNER
java -Xmx6g -jar kggseq.jar
--nt 4 --no-web --vcf-file examples/simu100.coding.vcf.gz --ped-file
examples/simu100.ped --out test1 --excel --db-filter
gadexome.eas,gadgenome.eas,1kgeas201305 --rare-allele-freq 0.01
--min-case-control-freq-ratio 3 --qqplot --gene-freq-score eas --db-score
dbnsfp --disease-causing-predict best --uwrunner-gene-coding
7.
Burden test by RUNNER and search
related papers in PubMed
java -Xmx6g -jar
kggseq.jar --nt 4 --no-web --vcf-file examples/simu100.coding.vcf.gz
--ped-file examples/simu100.ped --out test1 --excel --db-filter
gadexome.eas,gadgenome.eas,1kgeas201305 --rare-allele-freq 0.01
--min-case-control-freq-ratio 3 --qqplot --gene-freq-score eas --db-score
dbnsfp --disease-causing-predict best --runner-gene-coding --phenotype-term
schizophrenia --pubmed-mining-top-gene 10
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