DOWAS is a perl script for find potential off-target sites from reference and germline sequencing data in human. It consists of three pl scripts, run.pl will invoke other 2 scripts. All information you need to input should be written in a xml file like example.xml and run ‘perl run.pl example.xml 12’ in your computer. in that case, DOWAS will generate a folder in current path with same name with xml file (in that case it names ‘example’) and put all results in this folder and this software will use 12 threads. You need to install some software and write them in the xml file before using DOWAS, those softwares with recommend version are list at the end of this manual. Xml file contain a ‘rawdata_list’ subtag, it at least contains a father tag and a mother tag which contain raw sequencing data from parents in germline. Final result will be saved in /your/path/example/$offspring/final_result.txt, you will get multiple offspring folder and multiple final_result.txt if you have more than one offspring.
- DOWAS1 use public reference(e.g. hg19) as mapping reference, that may lead to illusory off-target sites due to private variants in individuals.
- DOWAS1 use a hard filter (mismatch<= 6 with PAM=NGG and mismatch<= 4 with PAM=NAG) to judge if a variant is an off-target site.
- DOWAS1 cannot detect large deletions (deletions larger than 150bp in 20 kilo bases around on-target site).
- DOWAS1 doesn’t report SNPs due to high false positive ratio.
- DOWAS1 cannot demonstrate the coverage at each potential off-target region directly.
- DOWAS1 doesn't consider hotspots predicted by experimental methods.
- The scalability of DOWAS1 is not good.
To overcome those shortage, DOWAS2 is developing and it can cover shortage 1,3,5,6,7 in DOWAS1.
cd /your/path
tar czvf DOWASv1.0.4.tar.gz
cd DOWAS v1.0.4
perl run.pl example.xml thread_num
DOWAS is released under MIT license. The latest version of DOWAS can be downloaded at www.sustc-genome.edu.cn.
fastp 0.19.4
samtools-1.9
jre-1.8.0_181
GATK-3.8
GATK-4.0.4.0
bwa-0.7.17
dbsnp database
OneKG_indel database
Mills_indel database
Human genome sequence reference
If you have questions about DOWAS, you may send the questions to [email protected] or [email protected] or [email protected] or caow@[email protected] . You may also ask questions in forums such as BioStar and SEQanswers.
We remove the dependency software in DOWAS package to reduce the size of DOWAS and avoid copyright problem, now you need to download those specified version softwares and write address of them in configuration xml file.
We changed sequence extract function in our code to reduce about one day’s DOWAS running time.
We add a thread number parameter to let user choose a suitable thread number to run DOWAS. And we use pipeline in mapping period to reduce IO spending.
We remove force parents data need. Now you can use offspring data with 1 parent or no parents to run DOWAS1.
DOWAS is written by Chen Kaijing, Chen Yangran, ChenRui and Cao Wei.
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