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Miaoxin Li (limx54@163.com)
Reference:
https://pmglab.top/kggseq/doc10/UserManual.html
Input data:
1.
A somatic variant summary file of breast
cancer [compiled from tumor portal http://www.tumorportal.org/tumor_types?ttype=BRCA]
examples/hg19_BreastAdenocarcinoma.maf
Purpose: Identify
cancer-driver genes of breast cancer
Run the commands step by step to see what will happen
1.
Annotate sequence variants by gene
models from RefGenes and GENCODE:
java -Xmx6g -jar kggseq.jar
--maf-file examples/hg19_BreastAdenocarcinoma.maf --out test1 --excel --db-gene
refgene,gencode --gene-feature-in 0,1,2,3,4,5,6,7
2.
Detect cancer-driver genes based on
somatic mutation rates at non-synonymous variants by ITER
java -Xmx6g -jar kggseq.jar
--maf-file examples/hg19_BreastAdenocarcinoma.maf --out test1 --excel --db-gene
refgene,gencode --gene-feature-in 0,1,2,3,4,5,6,7 --qqplot --iter-gene-coding
3.
Detect cancer-driver genes based on
somatic mutation rates at non-synonymous variants by WITER
java -Xmx6g -jar kggseq.jar
--maf-file examples/hg19_BreastAdenocarcinoma.maf --out test1 --excel --db-gene
refgene,gencode --gene-feature-in 0,1,2,3,4,5,6,7 --qqplot --witer-gene-coding
--db-score dbnsfp --cancer-mut-predict --witer-gene-coding
4.
Detect cancer-driver genes based on
somatic mutation rates at non-synonymous variants by WITER with a reference
for background gene mutation
java -Xmx6g -jar kggseq.jar
--maf-file examples/hg19_BreastAdenocarcinoma.maf --out test1 --excel --db-gene
refgene,gencode --gene-feature-in 0,1,2,3,4,5,6,7 --qqplot --db-score
dbnsfp --cancer-mut-predict --witer-gene-coding --ref-mut-file examples/Ovarian.gene.mutationburden.txt
5.
Detect cancer-driver genes based on
somatic mutation rates at non-synonymous variants by WITER and annotate
variants COSMIC
java -Xmx6g -jar kggseq.jar
--maf-file examples/hg19_BreastAdenocarcinoma.maf --out test1 --excel --db-gene
refgene,gencode --gene-feature-in 0,1,2,3,4,5,6,7 --qqplot --db-score
dbnsfp --cancer-mut-predict --witer-gene-coding --cosmic-annot
6.
Detect cancer-driver genes based on
somatic mutation rates at synonymous variants by ITER
java -Xmx6g -jar kggseq.jar --maf-file
examples/hg19_BreastAdenocarcinoma.maf --out test1 --excel --db-gene
refgene,gencode --gene-feature-in 0,1,2,3,4,5,6,7 --qqplot --response-gene-feature
7 --explanatory-gene-feature - --iter-gene-coding
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