Input data:
1.
A toy VCF file, examples/assoc.hg19.vcf.gz
2. A
conventional pedigree file, examples/assoc.ped
3. A
text file containing functional sets of genes, examples/geneset.txt
Purpose: Identify
potential pathogenic rare variants, genes and pathways for schizophrenia
Run the commands step by step to see what will happen
1.
Annotate sequence variants by RefGenes,
and GEncode models:
java -Xmx6g -jar kggseq.jar
--nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file examples/assoc.ped
--out test1 --excel
2.
Pathogenic predictions at non-synonymous
and non-coding variants
java -Xmx6g -jar kggseq.jar
--nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file examples/assoc.ped
--out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant
3.
Association at rare and low-frequency variants
java -Xmx6g -jar kggseq.jar
--nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file examples/assoc.ped
--out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant --var-assoc
--qqplot
4.
Association at rare and low-frequency variants
by RVTest
java -Xmx6g -jar
kggseq.jar --nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file
examples/assoc.ped --out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant --qqplot
--rvtest-var --rvtest-vcf --phe
disease1 --cov sex,age
5.
Association at rare variants of genes
by SKAT
java -Xmx6g -jar kggseq.jar
--nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file examples/assoc.ped
--out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant --db-filter
1kg201305 --rare-allele-freq 0.01 --qqplot --skat-gene --skat-cutoff 5 --phe disease1 --cov sex,age
6.
Association at rare variants of genes
by RVTest and search related papers in PubMed
java -Xmx6g -jar
kggseq.jar --nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file
examples/assoc.ped --out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant --db-filter
1kg201305 --rare-allele-freq 0.01 --qqplot --rvtest-gene --rvtest-vcf --phe disease1 --cov sex,age --phenotype-term
schizophrenia --pubmed-mining-top-gene 10
7.
Prioritize sequence variants by OMIM
information, phenolyzer and mouse phenotypes
java -Xmx6g -jar
kggseq.jar --nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file
examples/assoc.ped --out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant --db-filter
1kg201305 --rare-allele-freq 0.01 --qqplot --rvtest-gene --phe disease1
--cov sex,age --geneset-db cura --omim-annot --mouse-pheno
--phenolyzer-prediction --phenotype-term schizophrenia
8.
Association at rare variants of genesets
by SKAT
java -Xmx6g -jar
kggseq.jar --nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file
examples/assoc.ped --out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant --db-filter
1kg201305 --rare-allele-freq 0.01 --qqplot --skat-geneset --phe disease1 --cov sex,age --geneset-file examples/geneset.txt
9.
Association at rare variants of genesets
by RVTest
java -Xmx6g -jar
kggseq.jar --nt 4 --vcf-file examples/assoc.hg19.vcf.gz --ped-file
examples/assoc.ped --out test1 --excel --db-score dbnsfp,dbncfp_known --mendel-causing-predict
best --regulatory-causing-predict all --filter-nondisease-variant --db-filter
1kg201305 --rare-allele-freq 0.01 --qqplot --rvtest-geneset --rvtest-vcf --phe disease1 --cov sex,age --geneset-file
examples/geneset.txt
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