Small tutorial of kggseq for rare mutation burden test and phenotype relatedness estimation at genes in a schizophrenia sample

Miaoxin Li (limiaoxin@mail.sysu.edu.cn)

 

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