Reference:
http://grass.cgs.hku.hk/limx/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.
Two gene-network files downloaded
from http://giant.princeton.edu/download/,
frontal_lobe_top.gz and amygdala_top.gz.
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 --pheno-runner-gene-coding --phenotype-term schizophrenia ,hallucination --hpo-term HP:0000717 , HP:0000746 ,HP:0000738 --giant-net ./giant/ frontal_lobe_top.gz,./giant/amygdala_top.gz
2.
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 --pheno-runner-gene-coding --phenotype-term schizophrenia ,hallucination --hpo-term HP:0000717 , HP:0000746 ,HP:0000738 --giant-net ./giant/ frontal_lobe_top.gz,./giant/amygdala_top.gz
3.
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 --pheno-runner-gene-coding --phenotype-term schizophrenia ,hallucination --hpo-term HP:0000717 , HP:0000746 ,HP:0000738 --giant-net ./giant/ frontal_lobe_top.gz,./giant/amygdala_top.gz
--pubmed-mining-top-gene 10
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