Usage - shengqh/glmvc GitHub Wiki
[shengq1@cqs2 glmvc]$ mono glmvc.exe
General Linear Model Based Somatic Mutation Caller (GLMVC) - 1.3.0 - Quanhu SHENG ([email protected]/[email protected]) - CQS/VUMC
Those commands are available :
call Call somatic mutation and filter candidates by logistic regression model and annotate result
annotation Annotate mutation using varies tools.
validate Validate somatic mutation in vcf/bed file.
extract extract base composition of sites in vcf/bed file.
call
Call somatic mutation, filter candidates by logistic regression model and annotate result
[shengq1@cqs2 glmvc]$ mono glmvc.exe call
General Linear Model Based Somatic Mutation Caller (GLMVC) 1.3.0
--help Display this help screen.
--error_rate=DOUBLE (Default: 0.01) Sequencing error rate for
normal sample test
--glm_pvalue=DOUBLE (Default: 0.05) Maximum adjusted pvalue
used for GLM test
--annovar_set_default (Default: false) Set current setting as
annovar default setting
--annovar_buildver=STRING Annovar database version, for example:
hg19)
--annovar_db=DIRECTORY The directory contains annovar databases
--annovar_protocol=STRING Annovar protocols, for example:
refGene,snp138,cosmic68
--annovar_operation=STRING Annovar operation, must match with annovar
protocols, for example: g,f,f
--distance_insertion_bed=FILE Insertion bed file for distance
annotation.
--distance_deletion_bed=FILE Deletion bed file for distance annotation.
--distance_junction_bed=FILE Junction bed file for distance annotation.
--distance_exon_gtf=FILE Exon gtf file for distance annotation.
--rnaediting_db=FILE The rna editing database file
-t STRING, --type=STRING Required. Where to read/generate mpileup
result file (bam/mpileup/console)
--normal=FILE Bam file from normal sample (when
type==bam)
--tumor=FILE Bam file from tumor sample (when
type==bam)
-r STRING, --chromosomes=STRING (Default: all chromosomes in genome fasta
file) Chromosome names (separted by ',')
(when type==bam)
-m FILE, --mpileup=FILE Input samtools mpileup result file (when
type==mpileup)
-d INT, --read_depth=INT (Default: 10) Minimum read depth of base
passed mapping quality filter in each
sample
--fisher_pvalue=DOUBLE (Default: 0.05) Maximum pvalue used for
fisher exact test
--max_normal_percentage=DOUBLE (Default: 0.01) Maximum percentage of
minor allele at normal sample
--min_tumor_read=INT (Default: 5) Minimum read count of minor
allele at tumor sample
--min_tumor_percentage=DOUBLE (Default: 0.1) Minimum percentage of minor
allele at tumor sample
-c INT, --thread_count=INT (Default: 1) Number of thread, only valid
when type is bam
-o STRING, --output=STRING Required. Output file suffix
--no-BAQ=BOOL disable BAQ (per-Base Alignment Quality)
for samtools mpileup (when type==bam)
--read_quality=INT (Default: 20) Minimum mapQ of read for
samtools mpileup (when type==bam)
--base_quality=INT (Default: 20) Minimum base quality
-f FILE, --fasta=FILE Genome fasta file for samtools mpileup
(when type==bam)
annotation
Annotate mutation using varies tools.
[shengq1@cqs2 glmvc]$ mono glmvc.exe annotation
General Linear Model Based Somatic Mutation Caller (GLMVC) 1.3.0
Copyright (C) 2013-2015 Center for Quantitative Sciences/VUMC
--help Display this help screen.
-i FILE, --input=FILE Required. Input file generated by filter
function.
-o FILE, --output=FILE Output annotated file.
--annovar_set_default (Default: false) Set current setting as
annovar default setting
--annovar_buildver=STRING Annovar database version, for example: hg19)
--annovar_db=DIRECTORY The directory contains annovar databases
--annovar_protocol=STRING Annovar protocols, for example:
refGene,snp138,cosmic68
--annovar_operation=STRING Annovar operation, must match with annovar
protocols, for example: g,f,f
--distance_insertion_bed=FILE Insertion bed file for distance annotation.
--distance_deletion_bed=FILE Deletion bed file for distance annotation.
--distance_junction_bed=FILE Junction bed file for distance annotation.
--distance_exon_gtf=FILE Exon gtf file for distance annotation.
--rnaediting_db=FILE The rna editing database file
validate
validate somatic mutation sites using another normal/tumor paired data
[shengq1@cqs2 glmvc]$ mono glmvc.exe validate
General Linear Model Based Somatic Mutation Caller (GLMVC) 1.3.0
--help Display this help screen.
-v FILE, --validation_file=FILE Bed format file for somatic mutation
validation
--glm_pvalue=DOUBLE (Default: 0.05) Maximum adjusted pvalue
used for GLM test
--error_rate=DOUBLE (Default: 0.01) Sequencing error rate for
normal sample test
-t STRING, --type=STRING Required. Where to read/generate mpileup
result file (bam/mpileup/console)
--normal=FILE Bam file from normal sample (when
type==bam)
--tumor=FILE Bam file from tumor sample (when
type==bam)
-r STRING, --chromosomes=STRING (Default: all chromosomes in genome fasta
file) Chromosome names (separted by ',')
(when type==bam)
-m FILE, --mpileup=FILE Input samtools mpileup result file (when
type==mpileup)
-d INT, --read_depth=INT (Default: 10) Minimum read depth of base
passed mapping quality filter in each
sample
--fisher_pvalue=DOUBLE (Default: 0.05) Maximum pvalue used for
fisher exact test
--max_normal_percentage=DOUBLE (Default: 0.01) Maximum percentage of
minor allele at normal sample
--min_tumor_read=INT (Default: 5) Minimum read count of minor
allele at tumor sample
--min_tumor_percentage=DOUBLE (Default: 0.1) Minimum percentage of minor
allele at tumor sample
-c INT, --thread_count=INT (Default: 1) Number of thread, only valid
when type is bam
-o STRING, --output=STRING Required. Output file suffix
--no-BAQ=BOOL disable BAQ (per-Base Alignment Quality)
for samtools mpileup (when type==bam)
--read_quality=INT (Default: 20) Minimum mapQ of read for
samtools mpileup (when type==bam)
--base_quality=INT (Default: 20) Minimum base quality
-f FILE, --fasta=FILE Genome fasta file for samtools mpileup
(when type==bam)
extract
extract allele frequencies of predefined sites from single or multiple BAM files
[shengq1@cqs2 glmvc]$ mono glmvc.exe extract
General Linear Model Based Somatic Mutation Caller (GLMVC) 0.9.9.0
Copyright (C) 2013-2015 Center for Quantitative Sciences/VUMC
--help Display this help screen.
-v FILE, --bed_file=FILE Bed format file for sites
--bam_files=FILES Required. Bam files, separated by ','
--bam_names=STRINGS Required. Bam names, separated by ','
-o STRING, --output=STRING Required. Output file
--no-BAQ=BOOL disable BAQ (per-Base Alignment Quality) for
samtools mpileup (when type==bam)
--read_quality=INT (Default: 20) Minimum mapQ of read for samtools
mpileup (when type==bam)
--base_quality=INT (Default: 20) Minimum base quality
-f FILE, --fasta=FILE Genome fasta file for samtools mpileup (when
type==bam)
- example
mono glmvc.exe \
call \
-c 8 -t bam --max_normal_percentage 0.01 --glm_pvalue 0.05 \
-f hg19_16569_M.fa \
--rnaediting_db hg19.txt \
--annovar_buildver hg19 \
--annovar_protocol refGene,snp138,cosmic70 \
--annovar_operation g,f,f \
--annovar_db human_db \
--distance_exon_gtf Homo_sapiens.GRCh37.75.M.gtf \
--normal TCGA-A7-A0D9-RNA-NT.rmdup.split.recal.bam \
--tumor TCGA-A7-A0D9-RNA-TP.rmdup.split.recal.bam \
-o TCGA-A7-A0D9-RNA-TP-NT