varsim
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bioinform
VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
Hello, I would like to use VarSim to generate synthetic reads for structural variants from a given ground truth VCF file. To achieve this, I am using VarSim with the...
Hi, I've downloaded and built VarSim following the instructions on the documentation page. However, when I run the following code on my reference genome (I am using the hg38 reference...
Bumps commons-io from 2.4 to 2.7. [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a...
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Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.9.10.4 to 2.10.5.1. Commits See full diff in compare view [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter...
hello, thanks for the help. run build.sh came the error: ant zip-nojre Buildfile: build.xml does not exist! Build failed
Hi, I want to simulate only deletions on chromosome 22, between range 1-30 bps and 30bps to 1Mb. For the same I am using the following command: `python varsim.py --vc_in_vcf...
Hi, I am using Varsim for simulation and following is the command I am using: `python varsim/varsim.py --vc_in_vcf varsim/All_20170710_wdchr+header.vcf --sv_insert_seq varsim/insert_seq.txt --sv_dgv GRCh37_hg19_supportingvariants_2020-02-25_wdchr.txt --reference hg19/chr22.fa --id Simchr22 --read_length 125 --mean_fragment_size...
Hello All, This is not an issue, but I have a technical question. I wanna find the reads covered by each variant in the simulated truth VCF file. And I...
hello, when i run ./build.sh , it gives me this problem,could you tell me how to solve this problem? hope your answer [ERROR] Failed to execute goal org.codehaus.mojo:versions-maven-plugin:2.7:set (default-cli): Goal...
Hello Yunfei, This is probably an ART question rather than varsim but I have noticed that if you generate an error free sam by passing --art_options="--errfree" to varsim the generated...
