JAVA framework for accurate SNV assessment
Find source code and tools in the following sub-directories of the repository:
- src/ The main Java source code for JACUSA
- manual/manual.pdf The manual for JACUSA
- JacusaHelper R package to process JACUSA output file(s)
- tools/AddVariants Java tool to implant variants into BAM file
JACUSA has been developed and tested with Java v1.7.
IMPORTANT! Stranded paired-end data are handled properly with JACUSA v1.2.0 and higher. DO NOT USE JACUSA v1.0.1 on stranded paired-end data!
Get the current Jacusa JAR:
https://github.com/dieterich-lab/JACUSA/raw/master/build/JACUSA_v1.2.0.jar
v1.2.0
- Added support for stranded paired end reads - parameter -P changed
- Added support for single sample mode
- Added -R | --SHOW-REF option
- Minor fixes / typos
v1.0.1
- Minor fixes / typos.
DO NOT USE JACUSA v1.0.1 on stranded paired-end data!
https://github.com/dieterich-lab/JACUSA/raw/master/build/JACUSA_v1.0.1.jar
Since v1.2 the format of -P has changed! The format has been inspired by tophat's http://ccb.jhu.edu/software/tophat/manual.shtml library type parameter. With the command line parameter -P,--build-pileup the user can choose from combinations of:
- FR-FIRSTSTRAND STRANDED library - first strand sequenced,
- FR-SECONDSTRAND STRANDED library - second strand sequenced, and
- UNSTRANDED UNSTRANDED library.
Available methods for JACUSA $ java -jar jacusa.jar [ENTER]:
- call-1 Call variants - one sample
- call-2 Call variants - two samples
- pileup SAMtools like mpileup for two samples
General command line structure for variant calling call-1:
jacusa.jar call-2 [OPTIONS] BAM1_1[,BAM1_2,BAM1_3,...]
Get available options:
java -jar jacusa.jar call-1
General command line structure for variant calling call-2:
jacusa.jar call-2 [OPTIONS] BAM1_1[,BAM1_2,BAM1_3,...] BAM2_1[,BAM2_2,BAM2_3,...]
Get available options:
java -jar jacusa.jar call-2
Download and extract sample data
open https://cloud.dieterichlab.org/index.php/s/349PMjCdJl4wUwV
get hg19_chr1_gDNA_VS_cDNA.tar.gz
and unpack with
tar xzvpf hg19_chr1_gDNA_VS_cDNA.tar.gz
Call RNA-DNA differences (RDDs) by comparing gDNA and cDNA in sample data and save results in rdds.out.
$ java -jar call-2 -P UNSTRANDED,FR-FIRSTSTRAND -a H,M,B,Y -f 1024 -T 2.3 -p 2 -r rdds.out gDNA.bam cDNA1.bam,cDNA2.bam
Read, Process, and write JACUSA output files
Download JacusaHelper:
$ wget https://github.com/dieterich-lab/JACUSA/raw/master/JacusaHelper/build/JacusaHelper_0.43.tar.gz
Install JacusaHelper in R:
install.packages("JacusaHelper_0.43.tar.gz")
library("JacusaHelper")
Load JacusaHelper package in R:
library("JacusaHelper")
Read JACUSA output, filter sites where the variant base is NOT present in all replicates of at least one sample, and finally add editing frequency info:
# Read Jacusa output and filter by test-statistic >= 1.56 and
# ensure that site have at least 10 reads in (cov1) sample 1 and at least 5 reads per replicate in (covs2) sample 2
data <- Read("Jacusa_RDD.out, stat = 1.56, fields = c("cov1", "covs2"), cov = c(10, 5))
# This ensures that the variant base is present in all replicates of at least one sample
data <- FilterResult(data)
# This is only applicable for RDD calls and it will calculate their editing frequency.
# It is expected that gDNA is stored as sample 1!
data <- AddEditingFreqInfo(data)
Plot base change conversion:
# Among other additional infos, AddEditingFreqInfo will populate baseChange field in data
tbl <- table(data$baseChange)
barplot(tbl)
Check documentation in R for more details
?JacusaHelper
Add variants to a BAM file
Get the current AddVariants JAR:
$ wget https://github.com/dieterich-lab/JACUSA/raw/master/tools/AddVariants/build/AddVariants_v0.3.jar
Implant variants defined in <input.bam> into <variants.bed> and write results to <output.sam>:
java -jar AddVariants.jar <input.bam> <variants.bed> | samtools view -Sb - > <output.sam>
chr | start | end
see LICENSE file